תלמידת המחלקה להנדסה ביו רפואית לתואר שלישי תרצה בנושא:

Understanding and modeling mRNA translation based on ribosome profiling data

Gene expression is the process in which information encoded in the DNA is used to synthesize new proteins. Naturally, understanding, modeling and engineering this fundamental process has important contribution to every biomedical discipline, including human health and biotechnology. Gene expression has two major steps: transcription of the DNA to mRNA molecules and the translation of the mRNA molecules to proteins by molecular machines called ribosomes.

During mRNA translation ribosomes attach to the messenger RNA (mRNA) and then scan it in a sequential manner; each such scanning produces a new protein. Recently, a new experimental method - ribosome profiling was suggested for large scale study of ribosomal movement on the transcript. This method is based on next-generation sequencing and enables simultaneous estimation of the relative time ribosomes spend on the messenger RNAs of all translated transcripts in a genome, at a resolution of single nucleotides.

This work presents various new aspects of translation that were studied by analyzing ribosome profiles of thousands of genes in various organisms and their relation to translation efficiency.  Among others, I decipher the way biophysical properties of the mRNA molecules affect translation; I develop novel computational simulation of this experiment; and I suggest novel filters for analyzing these data. The reported results should improve the understanding of the translation process and also contribute towards developing new methods for gene expression engineering.

The talk is mainly based on four papers published in the recent years:  Dana and Tuller, PLoS Comput Biol. 2012; Dana and Tuller, Nucleic Acids Res. 2014; Dana and Tuller, BMC Genomics. 2014; Dana and Tuller, G3. 2014.

העבודה נעשתה בהנחיית  דר' תמיר טולר, המחלקה להנדסה ביו-רפואית, אוניברסיטת תל-אביב

ההרצאה תתקיים ביום ראשון 04.01.15, בשעה 14:15,

בחדר 315, הבניין הרב תחומי, אוניברסיטת תל אביב

  Physical Electronics Dept.

You are invited to attend a lecture

By

Yoav Livneh

(M.Sc. student under supervision of Prof. Yossi Rosenwaks, Dr. Philip Klipstein,

School of Electrical Engineering, Tel-Aviv University, Tel-Aviv 69978, Israel)

On the subject:

Band Structure Calculation and Analysis

of Antimonide Based Type-II Superlattices

Superlattices are a kind of quantum structure, made up of alternating thin layers of two materials. By changing the layer widths of the individual materials in the superlattice, we can control the optical and electrical properties of the material (bandgap engineering). In recent years, InAs/GaSb type-II superlattices (T2SLs) have become a very attractive potential sensing material in photonic devices used for infrared sensing and imaging.

This work presents a new and effective model for the prediction of T2SL band structure and absorption spectra, based on the k.p method, including a novel approach to the effect of the interfaces between the two individual materials. The main difference between this method and other k.p based methods is in the operator ordering, and in the use of delta-function like interface potentials. The model has reduced the number of fitting parameters to only six, all of which can be deduced empirically.

Calculation results show very good agreement with measurements on over 30 samples grown by Molecular Beam Epitaxy, both in the band gaps and the absorption spectra.

Thursday, 8 January 2015 at 09:30

Room 101, Software Eng. Build.