Archive
A happy first publication. A sad first publication.
Today, January 30th, 2013, my first co-first author primary paper was published online in Genome Biology. A long road from conception to a final product. Center stage for the conception was Simon Chan. Also for him is this a first: his first posthumous paper.
Simon joined UC Davis as a faculty member back in 2006 and not long after he arrived he started talking to Ian Korf. “Would it be possible to identify centromere tandem repeats from whole genome shotgun data?” Ian of replied in typical Ian style: “Sure, we’ll just write a Perl script to do the work for us!” And so the project was born, but at this stage it was not more developed as a human newborn baby would be.
282 species in a tree
The basic principle of the project was to identify and quantify the most abundant tandem repeats is the prime suspect to be the centromere tandem repeat. In 2006 is was strongly suspected that the centromeres of most animal and plant genomes consist of tandem repeats. Over time more and more evidence came forward that this indeed is true for most genomes, but certainly not all. In some species the centromeres consist of chromosome-specific sequences or unique sequences. In other cases several different tandem repeat sequences occupy the centromeres. And it gets even more bizarre when you think about species such as Caenorhabditis elegans. C. elegans’ chromosomes lack a primary constriction and thus a classic centromere. Rather the spindles bind along the entire length of the chromosome to unique sequences. These holocentric chromosomes are more common than often appreciated, as we review in another paper.
A few rotation students started to make some leeway, and once I did my rotation the very basic principles were just proven. Now it was time to expand it multiple genomes. First we focussed on WGS data obtained via old-fashioned Sanger sequencing. At this time I also had joined both Simon’s and Ian’s labs. We expended to genomes sequenced by Illumina or 454 sequencing. The sequences obtained by these next-generation platforms pose a new problem. We had to assemble those sequences most people throw in the trash, as they care more about genes than about junk DNA. And we explicitly wanted to get our hands on the junk DNA. Help came from DeRisi lab. DeRisi’s postdoc Graham Ruby was writing PRICE, a short-read assembler that allows you to align imperfect reads. Exactly what we needed, as the sequence variation of each individual repeat can be over 30% (on a stretch of 170 bp).
After 3 years of hard work we had data of 282 species. Sure, we did some PacBio sequencing ourselves (and help from PacBio and the sequencing core at UC Davis and Tim Smith at the USDA Meat Animal Research center). This data was very useful for identifying very very long tandem repeat found in bovine species. Now we had to make sense of the data. This would be much easier if we were looking at genes, but we aren’t. We look at repetitive DNA in tandem. To simplify our analysis we focussed on the consensus repeat sequences, but even that did not make things much easier. The problem remained that most sequences are too different to be compared. This observation was in line with published work: centromere DNA is very fast evolving. Even the point centromere of Saccharomyces cerevisiae where its 125 bp large centromere is evolving 3 times faster than non-selected stretches of DNA in its genome. Of course we also looked at various theories on centromere evolution and we found that our data is compatible with both predominant theories: centromere female meiotic drive and the library hypothesis.
We wrote the paper and went through many versions, mainly because Simon decided that writing it different would make it better (and usually did). Sadly Simon was only directly involved in the first submission. Just before he was hospitalized I took care of the second submission. The third and final submission, Simon never knew about as he had already died. That is what makes this his first posthumous paper, accompanied by Luca Comai’s comments. Thrilled it is published, but sad I cannot share the joy with the person who started the project back in 2006.
Melters DP, Bradnam KR, Young HA, Telis N, May MR, et al Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. Genome Biology 14: R10
Gut microbiota changes during pregnancy
Last month saw publication of the Human Microbiome Project Consortium detailing the breadth and depth of the human microbiome. http://www.nature.com/nature/journal/v486/n7402/full/nature11234.html This month in Cell there is an interesting article describing what happens to gut microbiota during pregnancy. Host remodeling of of the gut microbiome and metabolic changes during pregnancy. While cause and effect still need to be teased apart, it appears that late in pregnancy the gut microbiome of pregnant females appears more similar to changes seen in individuals with metabolic syndrome.
Building the Perfect Sandcastle
Finally a sandcastle that will remaining standing when the tide comes in.
Have you ever wondered what forces cause your perfectly sculpted turret to collapse suddenly? Or have you tried to find that optimum balance between sand, water, and compaction in order to get your sandcastle to stand tall and strong? If so, science has now defined various parameters to help you in your quest: “How to construct the perfect sandcastle“. My favorite part is that they built an underwater sandcastle using hydrophobic sand- rather than water acting as bridge between individual granules, air acts as the bridge. (See above picture). Now maybe I can finally convince my PI that a beach trip is a critical part of my thesis research…
Why are breeder tomatoes pale?
Figure 1a from the paper showing uniform green tomato fruit and fruit with green-shoulders.
Ever wonder why tomatoes you buy in the store have a uniform red color? A mutation in the transcription factor SIGLK2 has been bred into almost all the strains grown commercially. In an article out today, Dr. Ann Powell and colleagues show that SIGLK2 controls chloroplast development in tomato fruit, and a functional SIGLK2 leads to dark green fruit with dark shoulders. Increased chloroplast development leads to higher sugar levels in the fruit, and could affect taste (although they did not check that). Next time you are planning one of the recipes from our recipe section (http://bmcdb.wordpress.com/science-food/) pick out tomatoes that have dark shoulders if you want ones that don’t carry the mutation.
http://www.sciencemag.org/content/336/6089/1711.full
http://news.sciencemag.org/sciencenow/2012/06/how-tomatoes-lost-their-taste.html
How the Scientific Publishing Business works
This cute bear wants to publish his paper after 10 months of hard work and he faces the scientific publishing business and their restrictions....
"I'm so mad right now, I could through a marshmallow at you". Best quote ever!
(h/t @sciencecomedian)
BMCDB Recent Publication: Damian Guerra
The ubiquitin E3 ligase LOSS OF GDU 2 is required for GLUTAMINE DUMPER 1- induced amino secretion in Arabidopsis
- Rejane Pratelli1 (pratelli{at}vt.edu),
- Co first author Damian D Guerra2 (ddguerra{at}ucdavis.edu), <—– (BMCDB Student, Callis Lab UCD)
- Shi Yu1 (shiyu{at}vt.edu),
- Mark Wogulis3 (mawo{at}novozymes.com),
- Edward Kraft4 (ealkraft{at}gmail.com),
- Wolf B Frommer5(wfrommer{at}stanford.edu),
- Judy Callis2 (jcallis{at}ucdavis.edu) and
- Guillaume Pilot16 (gpilot{at}vt.edu)
Abstract
Amino acids serve as transport forms for organic nitrogen in the plant and multiple transport steps are involved in cellular import and export. While the nature of the export mechanism is unknown, over-expression of GLUTAMINE DUMPER 1 (GDU1) in Arabidopsis thaliana led to increased amino acid export. To gain insight into GDU1’s role, we searched for ethyl-methanesulfonate suppressor mutants and performed yeast-two-hybrid screens. Both methods uncovered the same gene, LOSS of GDU 2 (LOG2), which encodes a RING-type E3 ubiquitin ligase. The interaction between LOG2 and GDU1 was confirmed by GST pull-down, in vitro ubiquitination, and in planta co-immunoprecipitation experiments. Confocal microscopy and subcellular fractionation indicated that LOG2 and GDU1 both localized to membranes and were enriched at the plasma membrane. LOG2 expression overlapped with GDU1 in the xylem and phloem tissues of Arabidopsis. The GDU1 protein encoded by the previously characterized intragenic suppressor mutant, log1-1, with an arginine in place of a conserved glycine, failed to interact in the multiple assays, suggesting that the Gdu1D phenotype requires interaction of GDU1 with LOG2. This hypothesis was supported by suppression of the Gdu1D phenotype after reduction of LOG2 expression using either artificial miRNAs or a LOG2 T-DNA insertion. Altogether, in accordance with the emerging bulk of data showing membrane protein regulation via ubiquitination, these data suggest that the interaction of GDU1 and the ubiquitin ligase LOG2 plays a significant role in the regulation of amino acid export from plant cells.
Note: Anyone else in BMCDB who has published recently, please let us know so we can help get the good word out!
First successful artificial windpipe from stem cells
A week late, but For all the stem cell researchers out there, we now have a windpipe made from stem cells.
From MedlinePlus by Mary Elizabeth Dallas:
WEDNESDAY, Nov. 23 (HealthDay News) — A 36-year-old husband and father of two children with an inoperable tumor in his trachea (windpipe) has received the world’s first artificial trachea made with stem cells.
A report published online Nov. 23 in The Lancet described the transplant surgery, which was performed in June at the Karolinska University Hospital in Stockholm, Sweden.
Without the transplant, the authors of the report explained, the man from Reykjavik, Iceland would have died. A golf ball-sized tumor on his trachea had begun to restrict his breathing. In a 12-hour procedure, doctors completely removed the affected area of his trachea and replaced it with an artificial one.
The artificial trachea was custom-made using three-dimensional imaging. First, a glass model was built to help shape an artificial scaffold. Stem cells were then inserted into the scaffold to create a functioning airway, the authors explained in a journal news release.
The scientists said their technique is an improvement over other methods because they used the patient’s own cells to create the airway so there is no risk of rejection and the patient does not have to take immunosuppressive drugs.
In addition, they noted, because the trachea was custom-made it would be an ideal fit for the patient’s body size and shape, and would eliminate the need to remain on a waiting list for a human donor.
“The patient has been doing great for the last four months and has been able to live a normal life. After arriving in Iceland at the start of July, he was one month in hospital and another month in a rehabilitation center,” a co-author of the study and the physician who referred the patient for the procedure, Tomas Gudbjartsson, of Landspitali University Hospital and University of Iceland, Reykjavik, said in the news release.
Read the complete news article here. Read the proof of concept manuscript via The Lancet.
Monbiot’s critique on academic publishers
Last Monday (2011-08-29) in the Guardian, George Monbiot wrote a critique on academic publishers. He was shocked that this branch of the industry seems to fairing rather well in the current economic crisis (dip 2 and counting). Elsevier had an operating profit margin of 36% and charges a university library over $20,000 for Biochimica et Biophysica Acta. More surprisingly, Elsevier’s operating profit margin now is the same as it was in 1998. It is not these actual numbers that are the biggest problem (although the subscription money is decimating libraries’ budgets and thus the service they can provide). It is where they get the money from.
In short, researchers pay to publish in journals, where their peers perform quality control for these journals for free, and subsequently the journals demand money from everyone who would like to read these articles that passed the quality control.
The money the researchers use to pay for this (directly for their publication or indirectly through their institutions library to read their colleagues’ work) comes from their grants. Most of these grants come from public sources, such as the NIH and NFS grants. For individual and less fortunate universities (especially smaller and foreign ones) have to pay per individual article. How much do Elsevier, Wiley, Springer, NPG, etc. charge per article? Between $20-$42! There are exceptions such as Open Access journals (PLoS, BioMed Central, etc) or other forms of free pre-print (non peer-reviewed) sharing such as arXiv, but as the most prestigious journals: Nature, Science and Cell are not Open Access. The hard labor done by researchers with public money remains hidden behind corporate pay-walls. Why would companies be allowed to make so much money from public funds, while the People cannot access what they already paid for through taxes? It is not that these publishers are adding something to the acquired knowledge, as they ask the same people who write the article to review their colleagues work for free. Or so Monbiot argues.
Apparently Monbiot hit a nerve as this article went viral in the blogosphere. Below you can find some of the links to several responses to Monbiot’s article.
Some of the responses: WEIT. Gigaom. Noah Gray. The Chronicle of Higher Education.
Also, Jonathan Eisen, a UC Davis professor is trying to make his dad’s publications freely available, but he also encounters these very same problems.
Edit 1: SciELO (Open Access papers available)
Edit 2: A second article in the Guardian on academic publishers by Ben Goldacre.
CDK-1 inhibits meiotic spindle shortening and dynein-dependent spindle rotation
Recently, Marina Ellefson published together with her PI, Frank McNally, a paper in the Journal of Cell Biology.
Cytoplasmic dynein is a large multi-subunit molecular motor that is required for many cellular processes including spindle positioning. In the nematode C. elegans, cytoplasmic dynein is required for positioning the acentrosomal female meiotic spindle at the cell cortex prior to anaphase chromosome segregation. This dynein-dependent event occurs at a precise time during meiosis and is under cell cycle control, requiring activation of the anaphase-promoting complex (APC). In this study, we treated metaphase-arrested embryos with a small molecule inhibitor and found that cyclin B/CDK-1, a cell cycle driver and APC substrate , inhibits dynein-dependent meiotic spindle positioning. Inhibition of CDK-1 results in increased microtubule binding of the dynein activator, dynactin, suggesting that cyclin B/CDK-1 inhibits dynein-dependent spindle positioning via reducing the microtubule binding affinity of dynactin. This novel mechanism of cell cycle dependent regulation of cytoplasmic dynein may be important of other dynein driven processes.
Link to the original paper.
3D structure of HIV envelope protein sheds light on first contact between virus and cell
by Carlos Moscoso (Cheng lab)
The lab of Dr. R Holland Cheng focuses on the structural biology of viruses via cryoelectron microscopy (cryoEM), and its scope of interest includes HIV. Recently, we published a paper in PNAS outlining the structure of an immunogen based on the HIV envelope protein, which was rationally designed as a vaccine candidate. Using the single particle reconstruction technique, we derived a three-dimensional density map of the gp140 immunogen. The paper outlines the changes that the trimeric, fan-shaped complex gp140 undergoes as a result of ligand binding, including exposure of crucial conserved binding sites and promotion of host and viral membrane fusion. By comparing the gp140 complex in its native, unliganded state with gp140 bound to its receptor, key differences in quaternary structure were analyzed.
The primary observations gleaned from our comparison were that the interaction between each trimeric arm and the central stalk was weakened after binding to CD4, that the trimer undergoes some flattening, and that the subunits in each “fan blade” rotate to expose a previously cryptic binding site. These findings allowed us to devise a model for membrane fusion whereby the weakening of interaction between subunits facilitates refolding of the central stalk protein, allowing for juxtaposition and subsequent fusion of the viral and host cell membranes. Such a model provides the rationale behind the steps following this crucial first contact between virus and cell. Increased understanding of the membrane fusion events will facilitate virologists looking for ways to thwart them, as well as enhance rational vaccine design of an immunogen capable of inducing potently and broadly neutralizing antibodies.
The article in PNAS can be found here.
Quaternary structures of HIV Env immunogen exhibit conformational vicissitudes and interface diminution elicited by ligand binding. Moscoso CG, Sun Y, Poon S, Xing L, Kan E, Martin L, Green D, Lin F, Vahlne AG, Barnett S, Srivastava I, Cheng RH. Proc Natl Acad Sci U S A. 2011 Apr 12;108(15):6091-6. Epub 2011 Mar 28. PMID: 21444771
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