~~Computational solutions in interferometric and
tomographic imaging of live cells
גילי דרדיקמן תלמידת המחלקה להנדסה ביו רפואית לתואר שלישי
 
Imaging biological cells in vitro is imperative for both medical diagnosis and biological research. Quantitative phase-contrast interferometric microscopy holds great promise, as the phase delay measured in this method does not only supply good contrast, but also consists of valuable information regarding both the internal geometrical structure and the refractive index (RI) distribution of the sample. Nevertheless, phase-contrast microscopy suffers from several problems, keeping it from becoming the method of choice for biological imaging. In this research, we attempted to tackle some of the main issues: the phase unwrapping problem, meaning that the phase obtained is a modulo 2π function of the true phase profile; the coupling problem, meaning that the geometrical thickness and RI information are coupled in a way that makes it difficult to decipher each of these properties separately; and the computational efficiency problem, inhibiting real life applications such as real-time 3-D visualization.

העבודה נעשתה בהנחיית פרופ' נתי שקד , המחלקה להנדסה ביו-רפואית, אוניברסיטת תל-אביב

ההרצאה תתקיים ביום ראשון 08.04.18, בשעה 14:00
בחדר 315, הבניין הרב תחומי, אוניברסיטת תל אביב

Computational modeling of gene expression based on high-throughput NGS data
Alon Diament
Computational modeling of gene expression mechanisms is crucial to the understanding and the design of every biological system and enables the engineering of synthetic systems containing artificially regulated cellular processes. The presented studies are aimed at developing models of gene expression based on analysis of high-throughput next generation sequencing (NGS) data. Specifically, they focus on: (1) The principles that determine the evolution of the 3D organization of genes in genomes; (2) improving the measurement and modeling of translation and transcript evolution; and (3) applying computational models for the purpose of gene expression engineering.
We have shown, by analyzing high-resolution chromosome conformation capture data (Hi-C) from 5 eukaryotes, that the 3D organization of genes is strongly associated with their function, expression and codon usage (Diament et al., Nat Commun, 2014). In order to study the hypothesis that 3D organization and gene function co-evolve developed a computational approach for studying the organization of multiple organisms in a unified model (Diament and Tuller, Nucleic Acids Res, 2017). Inter-organismal study of the organization of the S. cerevisiae and S. pombe genomes has demonstrated that conserved and diverged modules of spatially organized gene families exist in these genomes, and that such modules are related to conserved and diverged biological processes. Furthermore, we have shown that 3D reconstructions of the S. cerevisiae genome can be improved using predictions that are based on the organization of the S. pombe genome (Diament and Tuller, PLoS Comput Biol, 2015).
Ribosome profiling (or Ribo-seq) is currently the most popular experimental methodology for studying translation; it has been employed in recent years to decipher various fundamental gene expression regulation aspects. In order to understand the resolution and limitations of ribosome profiling (Ribo-seq) we analyzed 15 datasets from 6 organism (Diament and Tuller, Biology Direct, 2016). We further developed an improved protocol for high resolution study of ribosome traffic during translation (Diament et al., PLOS Computational Biology, 2018). Our key finding using this protocol, was that ribosome traffic jams in S. cerevisiae are more frequent than previously thought. Our analysis also suggests that the yeast transcriptome may undergo selection for eliminating traffic jams.
Finally, we have developed algorithms and applied models of gene expression in order to engineer expression and adapt heterologous genes to a host (Diament et al., Submitted, 2018). Thus, the models and algorithms above can be employed to develop future biotechnological and biomedical applications.
העבודה נעשתה בהנחיית פרופ' תמיר טולר , המחלקה להנדסה ביו-רפואית, אוניברסיטת תל-אביב
ההרצאה תתקיים ביום ראשון 18.03.18, בשעה 14:00
בחדר 315, הבניין הרב תחומי, אוניברסיטת תל אביב
 

How engineering can breed value: the case of artificial ventilation
Prof. Yechiel. M. Barilan
Department of Medical Education
Sackler Faculty of Medicine

Abstract
Mechanical ventilation was invented as an aid to victims of polio who were conscious but unable to move their respiratory muscles. With the near extinction of polio, and the rise of intensive care medicine, today, most patients on respirators are critically ill and often sedated or unconscious.
The change in circumstances of use had implications on the design of respiratory machines and, consequently on the moral debate on disconnecting patients.

ההרצאה תתקיים ביום ראשון 11.03.18, בשעה 14:00
בחדר 315, הבניין הרב תחומי, אוניברסיטת תל אביב