מתן דודאי

תלמיד לתואר שני

המחלקה לפיזיקה באונ׳ ת״א

Modeling the migration behavior of cell colonies in two- and three- dimensions

Mechanotaxis is the directed migration of a cell due to forces it senses from the substrate, which are caused mainly by the presence of other cells or by external traction forces. The resulting cell movement plays important biological roles in, for example, wound healing, functions of the immune system, organogenesis or metastatic diseases. We present a model to simulate collective cell migration based on the forces that cells exert on elastic substrata. This work is focused on the influence of cell and substrate stiffness on the collective migration of cells. The simulations are initially developed to represent a two-dimensional (monolayer) problem, and then extended to represent migration in a three-dimensional extracellular matrix. The model is generic and can be utilized to study a variety of biological processes where migration is relevant, including tissue repair, cancer and infiltration of white blood cells to an infection site, to mention a few examples. 

~~(The talk will be given in English)

Speaker: Or Ordentlich
Institute for Problems in Mechanics, Moscow
Monday, March 23rd, 2015
15:00 - 16:00
Room 011, Kitot Bldg., Faculty of Engineering
A VC-dimension-based Outer Bound for the Zero-Error Capacity of the Binary Adder Channel
Abstract
The Binary Adder Channel (BAC) is a two-user multiple access channel whose inputs are binary and whose output is the real sum of the inputs. While the Shannon capacity region of this channel is well known, little is known regarding its zero-error capacity region, and a large gap remains between the best inner and outer bounds. In this work, we provide a new outer bound for this problem, improving the best known result by Urbanke and Li.
Our result is obtained via a confluence of combinatorial and information-theoretical arguments: Given any zero-error coding scheme for the BAC, we first construct another lower-dimensional coding scheme for the BAC with correlated messages. We then obtain a single letter outer bound for the Shannon capacity region of this more general setting, which translates back to an outer bound on the zero-error capacity of the BAC. Our construction is facilitated by introducing the notion of a "soft" VC-dimension of a codebook, which we lower bound by establishing a suitable variation of the Sauer-Perles-Shelah Lemma.

Joint work with Ofer Shayevitz.

ליאור טריימן

תלמידת המחלקה להנדסה ביו רפואית לתואר שני תרצה בנושא:

A computational study about the effect of oscillations in translation factors on translation rate

Gene  expression  is  a  central  cellular  process  by  which  the  protein  coding  potential inscribed in the DNA is converted into proteins. Translation, is an important step of gene expression. It is the process by which messenger RNA (mRNA) is decoded by a ribosome to produce a specific amino acid chain – protein. This fundamental process is related to all biomedical disciplines. Specifically, it may be engineered for various biotechnological applications. Oscillations and clocks are important components of many hardware systems, suggesting that they are required also in synthetic biology. As timing is a key factor in most engineered systems and also driving biological processes, this work focuses on the effect of oscillations on gene translation.

Effect of oscillations in tRNA pool levels, as well as oscillations in codon translation rates in different locations in the gene strand, were studied using the Totally Asymmetric Simple Exclusion Process (TASEP) as implemented in Matlab. This computational model takes into consideration the interactions between ribosomes and their size, concentration of tRNA molecules, efficiency of their interaction with codons, and the stochastic nature of translation.

 This is the first work done exploring oscillation in translation factors using simulations in a computational model that takes into consideration the bio-physical nature of translation process, it is a genome scale analysis using real data parameters including ribosome size, typical decoding times and real genes from the yeast genome.

Results suggest oscillating translation factors results in a periodic translation rate. A strong negative Spearman correlation (P<10^-87) exists between gene length and gene's translation rate amplitude. Moreover, the change of -10% in gene length has a stronger effect on translation rate amplitude (+34%) than in long genes (+9%). Furthermore, there is a strong positive Spearman correlation (P<10^-87) between the oscillated codon efficiency and genomic mean amplitude of translation rate, such that a change in +20% of oscillated codon velocity results in +40% increase and translation rate amplitude. In total about 200% change in translation rate amplitude is controlled by the oscillated codon velocity. Another connection was found between the relative locations of oscillation in the gene. When oscillating codons in the middle of the genes ORF it has a ~15% higher genomic mean amplitude comparing with oscillating codons on the edge (upstream) of the gene.

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

אוניברסיטת תל-אביב

ההרצאה תתקיים ביום ראשון 15.03.15, בשעה 14:15,

בחדר 315, הבניין הרב תחומי, אוניברסיטת תל אביב