2021 Global Biofoundries Alliance Webinar Series

GBA Webinar with Dr Rosalind Le Feuvre & Dr Mark Dörr

April 20th 2021 @ 1-2 pm CET

Watch The webinar here

https://studio.youtube.com/video/k8HdL4nndn

Dr Rosalind Le Feuvre

Director of Operations, SYNBIOCHEM and Future BRH, Manchester Institute of Biotechnology, UK

Rapid prototyping and automated strain engineering for next-generation sustainable biomanufacturing.

The application of predictive synthetic biology to rapidly engineer microbial cell factories promises to deliver new sustainable chemicals biomanufacture across industrial sectors (e.g., pharmaceuticals, green chemistry, novel materials, and advanced synthetic fuels).

In this Manchester Biofoundry talk I will discuss the development of an automated compound agnostic Design/Build/Test/Learn pipeline that integrates design software tools, automated build workflows and optimised analytical test screening to rapidly prototype microbial production routes for diverse chemicals/materials manufacture.

The transition from laboratory prototyping to production at scale and delivery of next-generation sustainable biomanufacturing processes requires major technical, scientific and economic challenges to be overcome.

Global Biofoundries will play a central role in the development of agile pipelines and reduce the delivery time from initial strain screening and prototyping towards industrial production that will accelerate the delivery of economically attractive, robust and scalable biomanufacturing processes to meet societal and commercial demand.

Dr. Mark Dörr

Head of LARA Platform, Institute for Biochemistry, University Greifswald, Germany

Robot and machine learning assisted protein engineering on the high-throughput screening platform LARA.

The University Greifswald robotic platform LARA (lara.uni-greifswald.de) is designed for high-throughput protein/enzyme screening. It consists of a central industrial robotic arm (Fanuc) serving 4 incubators (Thermo Cytomat 2), one centrifuge (Hettich Rotanta 460 R), one liquid handling station (Agilent bravo) and two plate readers (Thermo varioskan). Currently the platform is driven by Thermo's propitiatory control software Momentum. In my talk I will present our efforts to completely move towards python based open source solutions, only using open standards, like SiLA (sila-standard.org) and AnIML (animl.org). For this purpose, a free and open source software suite, the LARAsuite (gitlab.com/LARAsuite) is developed. It shall be used to plan and structure the current project with its project-management modules, operate the (automated) experiments with the LARA process manager (gitlab.com/opensourcelab/pythonlabscheduler) and finally store and visualize the data, fully supporting the requirements of the FAIR principles. The LARAsuite provides a semantically annotated database of most aspects of experimentation, it is therefore perfectly suited to structure and organize the data, including most information about the performed experiments. The LARAsuite also contains modules to exchange selected data sets and processes in a standardized way (SiLA, gRPC, SPARQL). These data exchange modules will be used to transfer automatable protocols, which are developed at one partner to the other partner. Lab- and automation processes are stored in a device-independent lab process description language (pythonLab, gitlab.com/opensourcelab/pythonLab). The process steps can then be mapped to a specific laboratory / lab automation system. With the mapping at hand, it is possible to execute the same processes on the target system, if all required lab instrumentation interfaces (SiLA servers) are available. This enables a transfer of processes from one laboratory to another platform.

Fellowship funding opportunities

Fellowship advice

The Department of Infectious Disease's mission is to apply excellent science and develop new approaches to address the unmet clinical needs for the control of infectious disease, both here in the UK and internationally. Our investigators study all aspects of infectious disease ranging from the fundamental science of microbial pathogens to the clinical outcomes of the infections they cause.

One of our key objectives as a Department is to inspire the next generation of infectious disease scientists, which includes developing the careers of our postdoctoral Fellows. We welcome all enthusiastic academics and practitioners to join our Department as Fellows. In particular, we encourage applications from female scientists and scientists from diverse backgrounds who are currently underrepresented within our academic and research community.

On this page, we will introduce to current Fellows in our Department, as well as signposting relevant funding opportunities and further guidance.

GBA Webinar with Tijana Radivojevic & Douglas Densmore

2021 Global Biofoundries Alliance Webinar Series January 27, 2021 1-2PM PST/4-5PM EST

Please join us for the first GBA webinar of 2021! Register in advance for this webinar by clicking here.

Tijana Radivojevic Data Scientist DOE Agile BioFoundry

Automated Recommendation Tool (ART) – Design of Experiments via probabilistic predictive modeling Synthetic biology allows us to bioengineer cells to synthesize novel valuable molecules such as renewable biofuels or anticancer drugs. However, traditional synthetic biology approaches involve ad-hoc engineering practices, which lead to long development times. We present the Automated Recommendation Tool (ART), a tool that leverages machine learning and probabilistic modeling techniques to guide synthetic biology in a systematic fashion, without the need for a full mechanistic understanding of the biological system. ART provides a set of recommendations for the next engineering cycle, alongside probabilistic predictions of their outcomes. It can be used as a python library or through a web-based graphical frontend that does not require coding expertise.

Douglas Densmore Associate Professor DAMP Lab DAMP Lab: Services, Workflows, and Infrastructure for Remote Synthetic Biology

In this talk I will outline the current state of the “Design, Automation, Manufacturing, and Prototyping” (DAMP) Lab at Boston University. This includes a software infrastructure for the execution of numerous experimental microbiology services, the analysis of the performance of these services, and a direct connection to the physical fabrication of low-cost microfluidics from high-level specifications. I will provide insight into several engagements that the DAMP Lab has been involved in as well as talk about how the DAMP Lab can contribute more to the Global BioFoundry Alliance (GBA) in 2021 and beyond.

Molecular insights into key drug target could help to enhance cancer treatments by Genevieve Timmins 13 November 2020

New research reveals how a key protein in cells could be tweaked to make cancer treatments more effective.

Radiation and chemotherapy are designed to kill cancer cells. However, for many patients, cancer cells can survive even after being hit with high doses. To make these treatments more effective, scientists are focusing on ways to tweak the inner machinery of cancer cells to make them more susceptible to dying.

A team of scientists at Imperial College London and Washington University School of Medicine in St. Louis is making headway in such efforts. In a new study published in Nature Structural & Molecular Biology, the researchers have identified how a key protein in cancer cells changes shape to kick-start the repair of DNA damage caused by chemotherapy or radiation. Blocking this built-in repair mechanism with a drug has the potential to make chemotherapy or radiation more effective, according to scientists.

As this protein is essentially the same in lower organisms as it is in people, the researchers studied the version of the protein found in yeast, called Mec1. Mec1 and its human counterpart, ATR, are switched on when cells are stressed. These proteins are responsible for sensing and repairing DNA damage before cells replicate to prevent that damage from being passed on to daughter cells.

Normally, this activation is good, protecting healthy cells from DNA damage that could lead to cancer. However, in other cases, such as cancer therapy, doctors would like to turn off these repair mechanisms to make cancer cells more susceptible to death by further DNA damage. In this way, cancer cells – hit with radiation and chemotherapy – can be destroyed more easily.

Video placeholder imagePlay video

The video shows two Mec1 molecules bound together (one is in colour on the left; the other is grey on the right). The side in colour shows how the protein moves to switch between active and inactive states.

The video shows two Mec1 molecules bound together (one is in colour on the left; the other is grey on the right). The side in colour shows how the protein moves to switch between active and inactive states. Credit: Luke Yates.

To understand how this protein functions, the Burgers Lab at the Washington University School of Medicine in St. Louis studied yeast with various mutations in this key protein. They discovered one mutant that forced the protein to be permanently switched on, but to identify how this was achieved, researchers needed to understand the molecular details.

Using high-resolution electron microscopes and cutting-edge detectors at the Electron BioImaging Centre and the Francis Crick Institute, researchers in the Zhang Lab at Imperial used the cryo electron microscopy technique to obtain high-resolution structures of both the native and mutant forms of the protein.

The molecular structures of both the inactive and active forms of this protein provide new insights into how changes from inactive to active take place, and how this protein is switched on to perform its vital functions. ATR kinase inhibitors are promising drugs for cancer treatment and the molecular structures provide the framework for improving current ATR kinase inhibitors or designing new ones.

Senior author Professor Xiaodong Zhang commented: “Cryo electron microscopy, a technique that won the 2017 Chemistry Nobel Prize, made it possible for us to visualize such complex large macromolecular machines in atomic details. Structures not only provide a molecular basis for how macromolecular machines function but are also required to explain how mutations cause disease, which will help with tailored treatment."

“We are grateful to the College, the generous funding from the Wellcome Trust, and our partners in London, which together have helped to establish the required cutting-edge infrastructure and made this type of work possible”.

Dr Luke A. Yates, a senior researcher in the Zhang lab and co-lead author, said: “Solving these large protein structures using cryogenic electron microscopy to such high-resolution has been a real career highlight (so far)."

"What was really wonderful to observe was how this relatively large protein twisted to place a small number of chemical groups (amino acid residues) into the correct position to allow it to perform its job. What is also quite neat is that these amino acid residues are held out of alignment to keep the protein turned off.”

Tannous EA, Yates LA, Zhang X, Burgers PM. Mechanism of auto-inhibition and activation of Mec1-ATR checkpoint kinase. Nature Structural & Molecular Biology. Nov. 9, 2020. DOI 10.1038/s41594-020-00522-0

This article was adapted from a press release by Washington University School of Medicine in St. Louis

Image credit: Anne Weston, Francis Crick Institute

DNA replication under the (electron) microscope

Article by Nadezhda Aleksandrova, MRes student at Imperial College London

Dr Alessandro Costa, a group leader at The Francis Crick Institute and an Imperial College alumnus, was the guest lecturer for the Imperial College Section of Structural Biology seminar in April. He presented his work, which is focused on understanding the molecular mechanisms underlying DNA replication in complex organisms such as animals and plants. DNA replication is a fundamental process that allows the entire DNA from a single cell to be copied and divided between two daughter cells when cell division occurs. The mechanism of replication is tightly regulated, as errors arising from copying the genetic code may result in accumulation of mutations within DNA and can subsequently drive cancer development.

 The main technique that Dr Costa’s lab uses to study the mechanisms of DNA replication is single particle- electron microscopy- a cutting-edge technique that allows scientists to visualise single proteins and protein assemblies in very high resolution, down to their building blocks, the amino acid residues. Researchers in Costa’s lab use the technique to model the small movements of the proteins responsible for DNA replication to understand what happens when a DNA strand binds to those proteins and how the process is facilitated by the energy currency of the cell, ATP.

 Initially, Dr Costa and his team were interested in helicase, the enzyme responsible for ‘opening up’ the DNA helix, and how it binds to a strand of DNA. This step is necessary, as the DNA is tightly wound into a double helix that cannot be copied without its structure being partially disrupted to allow for the necessary protein machinery to access the genetic code. The 3D images generated by the scientists at the Crick, shown in the figure below, show that helicase binding alone is not sufficient to separate the DNA strands from one another.

Subsequent research in Costa’s lab reveals that binding of ‘firing factors’ to helicases activates the proteins, triggering DNA unwinding. This occurs through ‘stretching’ of the DNA double helix by the active helicase, resulting in single-stranded DNA regions ready for duplication.

 In addition, Dr Costa’s group has generated a 3D model of how the long stretches of DNA move through the channel of the helicase. This allows the full length of the double helix to be sequentially opened up and copied rapidly and efficiently. Efficiency is key in this process, as cell division occurs in the matter of only an hour, during which a huge stretch of DNA must be copied without any mistakes.

 Apart from the work presented in the seminar, Dr Alessandro Costa is also involved in research on the replisome- the protein assembly that has the job of copying DNA. They also strive to improve sample preparation and analysis of electron microscopy images, as the quality of the sample and the image processing are fundamental for the quality of the resulting 3D structures. 

References: Cryo-EM structure of a licensed DNA replication origin, The mechanism of eukaryotic CMG helicase activation

"A New Lead in BMPRII Inhibition in Pulmonary Hypertension"

A new publication from a group of scientists including our very own Dr Luke Yates , a researcher in Professor Xiaodong Zhang’s research group, published their research on CLIC4 and BMPRII in pulmonary hypertension.

You can find the journal article here:

https://www.ahajournals.org/doi/10.1161/CIRCRESAHA.118.313705#.XDNptcjeVZ8.twitter

FASEB conference on Machines on Genes

Xiaodong Zhang and Luke Yates attended the FASEB Machines on Genes meeting last week in Snowmass, Colorado and Xiaodong Zhang gave a keynote lecture, and Luke's talk was well received.

Structure and regulation of the human INO80–nucleosome complex

By Rafael Ayala, Oliver Willhoft, Ricardo J. Aramayo, Martin Wilkinson, Elizabeth A. McCormack, Lorraine Ocloo, Dale B. Wigley & Xiaodong Zhang

Access to DNA within nucleosomes is required for a variety of processes in cells including transcription, replication and repair. Consequently, cells encode multiple systems that remodel nucleosomes. These complexes can be simple, involving one or a few protein subunits, or more complicated multi-subunit machines1. Biochemical studies2,3,4 have placed the motor domains of several chromatin remodellers in the superhelical location 2 region of the nucleosome. Structural studies of yeast Chd1 and Snf2—a subunit in the complex with the capacity to remodel the structure of chromatin (RSC)—in complex with nucleosomes5,6,7 have provided insights into the basic mechanism of nucleosome sliding performed by these complexes. However, how larger, multi-subunit remodelling complexes such as INO80 interact with nucleosomes and how remodellers carry out functions such as nucleosome sliding8, histone exchange9 and nucleosome spacing10,11,12 remain poorly understood. Although some remodellers work as monomers13, others work as highly cooperative dimers11, 14, 15. Here we present the structure of the human INO80 chromatin remodeller with a bound nucleosome, which reveals that INO80 interacts with nucleosomes in a previously undescribed manner: the motor domains are located on the DNA at the entry point to the nucleosome, rather than at superhelical location 2. The ARP5–IES6 module of INO80 makes additional contacts on the opposite side of the nucleosome. This arrangement enables the histone H3 tails of the nucleosome to have a role in the regulation of the activities of the INO80 motor domain—unlike in other characterized remodellers, for which H4 tails have been shown to regulate the motor domains.