TIDAL-Fly: a new database resource of Transposon Landscapes for understanding animal genome dynamics.

We tend to think of our genomes as nicely-ordered encyclopedias,  curated with only useful information that makes up our genes.  In actuality, nature and evolution is extremely sloppy.  All animal genomes, from us humans to the simple fruit fly, are littered with genetic baggage.  This baggage is sizeable, making up at least 11% of the fly genome and more than 45% of our genome.  The scientific term for this baggage is transposable elements (TEs) or transposons, which are mobile entities that must copy themselves to other places of the genome to ensure their survival during animal evolution.

Because there are so many copies of transposons, they can be difficult to analyze by most standard genetic methods. Brandeis postdoctoral fellow Reazur Rahman and a team in Nelson Lau’s lab have formulated a new tool called the Transposon Insertion and Depletion AnaLyzer (TIDAL). TIDAL aims to provide an accurate and user-friendly program to reveal how frequently transposons can move around in animal genomes.  Currently, the TIDAL tool has been applied to over 360 fruit fly genomes that have been sequenced and deposited in the NIH NCBI Sequencing Read Archive.  The outputs from this program are available to the whole genetics community through the TIDAL-FLY database.

tidal fly banner

The TIDAL-Fly database will allow geneticists to pick their favorite fly strain and see if a transposon has landed near to their gene and perhaps affect gene expression. Fruit flies are key model organisms utilized by many researchers, including here at Brandeis, to study human diseases, from infertility to insulin signaling to aging to sleep disorders.  Since these new transposon insertions are not available in the standard genome databases, this tool and website may provide answers to previously puzzling genetic effects not revealed by typical DNA sequencing studies.  It is Reazur’s and the Lau lab’s goal to continue updating the TIDAL-Fly database with more genomes as fly genome re-sequencing becomes easier and easier to perform.

see also: Rahman R, Chirn GW, Kanodia A, Sytnikova YA, Brembs B, Bergman CM, Lau NC. Unique transposon landscapes are pervasive across Drosophila melanogaster genomes. Nucleic Acids Res. 2015.

2 New Faculty Members Join Biochemistry

Tijana Ivanovic and Maria-Eirini Pandelia have joined the Biochemistry department. Both of the new faculty members will begin at Brandeis in January 2016.


tijana_photoTijana Ivanovic, is currently a postdoc at Harvard Medical School.  Stephen C. Harrison is her advisor. She received her PhD in Virology from HMS and her BS in Microbiology and Molecular Genetics from UCLA.

Her research focuses on uncovering fundamental molecular mechanisms of virus translocation across biological membranes, in the distinct contexts of enveloped-virus membrane fusion and nonenveloped-virus membrane penetration.  She applies and develops advanced biophysical and biochemical approaches and combines them with those of virology, molecular biology and cell biology.

Dr. Ivanovic received a grant from the L’Oréal USA For Women in Science fellowship program in 2011.


pandeliaMaria-Eirini Pandelia‘s ‘scientific journey’ started from Greece, where she received her undergraduate degree in Physics from the University of Patras and master of sciences degree in applied Mathematics and Physics from the National Technical University of Athens. She carried out her graduate studies in Germany at the Max-Planck Institute (MPI) of Chemical Energy Conversion (formerly known as MPI for Bioinorganic Chemistry) and received her doctoral degree from the Technical University of Berlin. This was followed by 3 years as a postdoc at PennState University in the Bollinger/Krebs laboratory.

Her research lies in the interface of Chemistry, Biology and Physics with particular focus on the study of metalloenzymes. Her work encompasses the combination of spectroscopic and biophysical techniques together with structural biology and phylogenetics to address the modus operandi of metalloproteins and bioinorganic complexes. Her main expertise is in Mössbauer and EPR spectroscopies coupled to time-resolved kinetics (optical, FTIR) and redox potentiometry. She is interested in understanding how diverse enzymes carry out their bio-transformations and how reaction selectivity in homologous proteins is achieved.

Maria-Eirini’s work at Brandeis will be centered on delineating the mechanisms according to which metalloproteins involved in processes essential for life perform the activation of small (or larger) molecules, how the specific identity of the metals in the active sites allows their chemical diversion and selectivity and what the functional role of iron-sulfur clusters in proteins involved in DNA synthesis and repair is.

 

 

 

 

 

Getting clotting factors to last longer in the blood

The BCH blog Vector talks about the progress of rFIXFc, a recombinant hybrid of Factor IX and an Fc receptor fragment, a new long lasting clotting factor which recently passed a phase 3 clinical trial. The technology is the result of a collaboration Wayne Lencer, a researcher at Boston Children’s Hospital, Richard Blumberg from Brigham and Women’s Hospital (BWH) and Associate Professor of Biology Neil Simister from Brandeis. We’re all excited to see this technology emerge from the labs, and progress to the point where it’s poised to make a significant impact in the lives of hemophilia patients.

Hall, Rosbash and Young Share Shaw Prize in Life Science and Medicine

The 10th annual Shaw Prize in Life Science and Medicine has been awarded jointly to Michael Rosbash and Jeffrey Hall of Brandeis and Michael Young of Rockefeller University. The trio are once again being honored for their discovery of molecular mechanisms underlying circadian rhythms. Hall is Emeritus Professor of Biology at Brandeis, and Rosbash is Peter Gruber Endowed Chair in Neuroscience, Professor of Biology, and Howard Hughes Medical Institute Investigator.

The Shaw Prize, established under the auspices of Mr Run Run Shaw, honours individuals, regardless of race, nationality, gender and religious belief, who have achieved significant breakthrough in academic and scientific research or applications and whose work has resulted in a positive and profound impact on mankind. There are three annual prizes: Astronomy, Life Science and Medicine, and Mathematical Sciences, each bearing a monetary award of one million US dollars. The presentation ceremony is scheduled for Monday, 23 September 2013.

Update: There a couple of really nice videos on YouTube from the Pearl Report (TVB in Hong Kong) that discuss the science and the history behind this prize.

Rosbash, Hall, and Young Honored with Canada Gairdner International Award

Brandeis science faculty members Michael Rosbash and Jeff Hall were named today as 2012 recipients of the Canada Gairdner International Award, one of the world’s top prizes for biomedical research. Together with Michael Young (Rockefeller Univ.), they were honored “for pioneering discoveries concerning the biological clock responsible for circadian rhythms”. The trio has previously been honored with the 2011 Louis Gross Horwitz Prize and the 2009 Gruber Neuroscience Prize for this research.

The Gairdner Foundation in Toronto began giving awards in 1959 to recognize and reward the world’s most creative and accomplished biomedical scientists. So far about a quarter of the recipients have gone on to win a Nobel Prize. Also honored this year (for other work) were neuroscientist Tom Jessell and immunologist Jeffrey Ravetch.

Hall is now Professor Emeritus of Biology, and his influence is felt strongly in the strong Drosophila genetics community at Brandeis even though his lab is gone. The Rosbash lab continues to be a force for innovation in research on circadian regulation and mRNA processing. To hear more about Rosbash lab research, come to Wednesday seminar on April 4, when Michael will be the speaker. The title of his seminar is: 37 years at Brandeis (but who’s counting): Gene Expression and Circadian Rhythms.

Here’s some video the Gairdner Foundation posted on YouTube:

More information about this story at the following sites:

From bench to clinical trials: the rFIXFc story

BrandeisNOW has a new story about the development of recombinant Factor IX Fc,  a candidate drug for hemophila, currently in Phase III cliniical trials. The story behind the Fc fusion technology started in academic labs including Neil Simister‘s at Brandeis, led to a biotech startup (Syntonix), which was then acquired by Biogen Idec, who are now conducing clinical trials.

For more, see http://www.brandeis.edu/now/2011/june/hemophilia.html

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