Methodology Round Tables

Experimental biologists often encounter a tremendous leap in methodologies that can significantly advance their ability to conduct state of the art competitive research. In this session, leading Israeli scientists will present 9 different modern methodologies in a round table format.  Each round table will present in detail the background and experimental design of the specific methodology, and include important controls, expected outcome, anticipated problems and provide further advice according to their own experience.

Please note that participation will require pre-registration on a first-come first serve basis.  A single registration per person and a limit of 12 participants per topic will be accepted by the system.  Once the limit is reached, the registration will be closed.

We encourage participants to contact the moderators and send questions at least two weeks prior to the session. Depending on the topic, participants may be offered to share their own data and experience in order to contribute to the productivity of the discussion.

The topics are:

  • 3-D Printing and Biology (Tal Dvir, Tel-Aviv University & Aryeh Batt, PreciseBio LTD)
  • Single Cell Genomics (Hadas Keren-Shaul, Weizmann Institute of Science and Merav Cohen, Weizmann Institute of Science)
  • Measuring Behavior (Lior Bikoveski, Tel-Aviv University; Galit Ofir, Bar-Ilan University and Michael Tsoory, Weizmann Institute of Science)
  • Metabolomics (Ilana Rogachev, Weizmann Institute of Science)
  • Meeting the Challenges of High Throughput Biology for Drug Discovery (Haim Barr, Weizmann Institute of Science and Wissam Mansour, AnimaBiotech LTD)
  • Proteomics (Tamar Ziv, Technion and David Morgenstern, Weizmann Institute of Science)
  • Flow Cytometry (Ziv Porat, Weizmann Institute of Science)
  • Protein Display Technologies (Itai Benhar, Tel-Aviv University)
  • Introduction to Microbiome Analysis (Omry Koren, Bar-Ilan University and Uri Gophna, Tel-Aviv University)

3-D Printing and Biology

Tal Dvir (George S. Wise Faculty of Life Sciences & Department of Materials Science and Engineering, Tel-Aviv University)

Aryeh Batt (PreciseBio LTD.)

In this roundtable we will present the concept of 3D printing of tissues for regenerative medicine. We will start by a short introduction on the history of 3D bioprinting and the basics of this concept, explaining the need for the technology and describing its impact on modern industry, medical practice and academic research. We will then discuss the different printing approaches, including extrusion, inkjet and laser-assisted technologies. The strengths and limitations of the different technologies will be described, with a focus on the capacity of each method to support fabrication of specific biological structures.  We will then try to envision the future of regenerative medicine and the role of advanced fabrication techniques, like 3D printing, in shaping the next generations of this field.  Finally, we will discuss latest advances and prominent recent research in the field, give an academic and industry’s perspective, and state the existing challenges in bringing these technologies to the clinic.

tdvir@post.tau.ac.il; aryeh.batt@precise-bio.com

Single Cell Genomics

Hadas Keren-Shaul (Life Sciences Core Facilities, Weizmann Institute of Science)

Merav Cohen (Department of Immunology, Weizmann Institute of Science)

Biological systems are highly complex and comprise of many heterogeneous cell populations that are difficult to decipher using conventional bulk methods. Single cell genomics enables analyzing complex tissues and organs with maximal resolution and minimal bias and has been revolutionizing our understanding of normal physiology and disease. Methods for single-cell genome-wide expression analysis are continuously being developed, offering increasing coverage, precision and throughput. In this workshop, we will cover several methodologies for single cell RNA-seq available today, which are based on microfluidics, Fluorescence Activated Cell Sorting (FACS), mechanical micromanipulation/micropipetting, laser capture microdissection and more. We will discuss the different platforms available for a single cell project and how to match between a biological model to the most appropriate single cell genomics technique. Moreover, we will describe the different computational algorithms available for the analysis of the large scale data derived from a single cell RNA-seq experiment. In addition to single cell transcriptional information, next-generation adaptations of single cell genomic methods are rapidly emerging; those involve the simultaneous recording and integration of complementary types of cellular and molecular information from the same cell. We will discuss some of these adaptations such as genome engineering, spatial reconstruction, cell-cell interactions, immune profiling and lineage tracing. Alongside transcriptional profiling, it is now also possible to acquire genetic information at the single cell level, providing a broader understating of the cellular state. We will mention some of these aspects such as single cell ATAC-seq and single cell copy number variations.

We encourage the workshop participants to submit a one-page abstract describing the biological question, and how single cell analysis can contribute to the study. The abstract should describe the working hypothesis, experimental design and any preliminary results. Selected abstracts, announced prior to the workshop, will be presented by the student (5 min powerpoint presentation) and discussed during the workshop for proper single cell experimental design and troubleshooting.

Hadas.Keren-Shaul@weizmann.ac.il; merav.cohen@weizmann.ac.il

Measuring Behavior

Lior Bikovski (The Myers Neuro-Behavioral Core Facility, Technion – Israel Institute of Technology)

Galit Shohat-Ophir (The Mina and Everard Goodman Faculty of Life Science, Bar-Ilan University)

Michael Tsoory (Behavioral and Physiological Phenotyping Unit, Department of Veterinary Resources, Weizmann Institute of Science)

The session is indented for participants that are new to the behavior field and are interested in acquiring knowledge on approaches and technologies used to measure behavior, and is also an opportunity for researchers form the behavior field who would like to enrich their knowledge and contribute from their own expertise to the discussion. We will present a series of behavioral paradigms and the technical considerations relevant for using existing assays and when designing new behavioral assays. We will demonstrate the use of machine vision and machine learning technologies to quantify behaviors, together with state of the art neurogenetic tools to dissect neuronal mechanisms. We will present disease model paradigms and discuss the process of phenotyping; planning experiments that allow the identification of altered or impaired brain functions while controlling confounding factors. In addition, we will discuss the challenges of standardization in behavioral neuroscience work, and how to successfully translate a working method from one lab (e.g. seen in a paper) to another.

liorbiko@gmail.com; galit.ophir@biu.ac.il; michael.tsoory@weizmann.ac.il

Metabolomics

Ilana Rogachev (Department of Plant and Environmental Sciences, Weizmann Institute of Science)

The goal of this round table is to give an overview of the metabolomics workflow and methodology. The following topics will be addressed: brief introduction to metabolomics techniques, analytical platforms and data analysis, focusing on liquid chromatography-mass spectrometry (LC-MS). We will discuss experimental design, sample preparation and quality controls in more details, as these are the main prerequisites for a successful experiment. The participants are invited to present examples from their own research and raise related challenges.

Ilana.Rogachev@weizmann.ac.il

Meeting the Challenges of High Throughput Biology for Drug Discovery

Haim Barr (Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science)

Wissam Mansour (AnimaBiotech LTD.)

Analysis and interpretation of large data sets has fueled rapid advances in biology, notably by increased understanding of multivariate patterns  in complex populations. While this has been vital in describing human disease, the discovery of novel disease modifying drugs has lagged behind. The purpose of this round-table is bring together scientists who are interested in closing the gap between drug target identification and drug discovery such that high throughput screening techniques may be applied to more tractable drug targets. Topics to be discussed will include:

  • Gene druggability – if we know so much about gene expression, where are all the targets?
  • Are all target druggable? 
  • Medicinal chemistry for drug discovery – we are on the road, but who is driving this car?
  • Closing the throughput gap – when does more actually become less ?
  • Emerging technologies to drive the process – AI as human friend 

Following the round-table we will discuss the possibility of launching a local special interest group to continue discussions throughout the year.

haim.barr@weizmann.ac.il; wissam.mansour@animabiotech.com

Proteomics

Tamar Ziv (The Smoler Protein Research Center, Faculty of Biology, Technion – Israel Institute of Technology)

David Morgenstern (Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science)

Proteomics is a powerful technique for identification and quantification of proteins. Combining high speed and high accuracy mass spectrometry with bioinformatics can benefit any proteomic project from large-scale comparisons between proteomes with their unique patterns of posttranslational modifications to simpler experiments like protein profiling and analysis of protein complexes.

First, we will discuss the design of different types of proteomics projects including repeats, controls and the optional analysis methods.

Second, we will present some key points for successful sample preparation for mass spectrometry. Unfortunately, instrumentational and computational limitations require the adjustment of sample preparation protocols for optimal results. Such adjustments are not trivial, and are often ignored or overlooked in the process of sample preparation, resulting in suboptimal results or failed experiments. We will focus specifically on IPs and gel-based proteomics which tend to suffer the most from inappropriate sample preparation. In addition, we will discuss the specific hurdles of samples prepared from tissues and body fluids.

Third, we will present some suggestions how to analyze and continue with the proteomics data.

tamarz@technion.ac.il ; david.morgenstern@weizmann.ac.il

Flow Cytometry

Ziv Porat (Flow Cytometry unit, Life Sciences Core Facilities, Weizmann Institute of Science)

Flow Cytometry has gained a major place as an analytical and preparative method in biological studies in the past 50 years. In principle, cells in suspension are labeled with fluorescent markers and are run in a single file through a flow cell, where they are illuminated by laser beams of different wavelengths. The light scattering as well as multiple fluorescence intensities are collected for each channel separately, allowing measurement of potentially 30+ parameters from each cell. The technology allows rapid collection of multi-parametric data for a large number of cells (up to 100 million cells). In addition, using cell sorters, specific populations can be separated for downstream analysis or processing.

Although the basic technology remaines similar, advances during the years include: higher powered lasers with a greater range of wavelengths, complex electronics increasing the speed of signal processing, increased variety of fluorescent stains and antibodies, complex software tools for data analysis, new fluorescent gene reporters, improved technologies of single cell isolation and the addition of hybrid technologies like Imaging Flow Cytometry, Mass Cytometry and spectral Flow Cytometry.

There are numerous applications for Flow Cytometry in immunology, cell biology, cancer research, however practically every discipline that involves studies at the cellular level utilizes this common technology. In this session, the basic principles of analysis and cell sorting by flow cytometry will be covered, as well as examples of its diverse usage and recent developments in this field.

Ziv.Porat@weizmann.ac.il

Protein Display Technologies

Itai Benhar (George S. Wise Faculty of Life Sciences, Tel-Aviv University)

In vitro selection technologies, also known as “protein display technologies” have transformed the development of research and therapeutic monoclonal antibodies. Using methods such as phage, ribosome, yeast display and cell display, high affinity binders can be selected from diverse repertoires. While protein display technologies are mainly applied for de-novo  antibody isolation, they are also being used for the improvement of existing binders (hits), to improve their binding affinity and specificity and to improve upon their developability. Protein display technologies may be used for non-antibody proteins as well, however, we will only mention those in brief.

During the roundtable, we will discuss strategies for the generation of antibody libraries and how antibodies are isolated from such libraries. We will focus on phage and yeast display systems, presenting the workflow, the advantages and the limitations of each approach. Finally we will briefly discuss the integration of next-generation sequencing (NGS) in the process of antibody isolation from antibody-display libraries.

The moderator encourages potential participant to contact him before the conference to bring up relevant issues they would like to have discussed during the roundtable.

benhar@tauex.tau.ac.il

Introduction to Microbiome Analysis

Uri Gophna (George S. Wise Faculty of Life Sciences, Tel-Aviv University)

Omry Koren (Azrieli Faculty of Medicine, Bar-Ilan University)

Microbiome analysis requires careful study design, standardized protocols, and advanced bioinformatic and statistical analysis. In this roundtable, we will discuss these issues and share our experiences, both good and bad, from the perspective of postdocs, PIs, reviewers and journal editors. Microbiomes of humans, rodents, insects and marine invertebrates will be covered.

urigo@post.tau.ac.il; omry.koren@biu.ac.il