Researchers Use Comet to Examine a DNA-Editing Enzyme

By Staff report

March 14, 2020

Genome editing stands to change the trajectory of human civilization, with massive implications for treatments of any genetic disease and potential for even broader improvements in human health. The process, however, is currently limited, difficult and expensive, with a number of different organizations exploring a variety of techniques. Now, chemists from the University of California San Diego have applied supercomputing in their quest to make genome editing more viable.

Using molecular dynamics simulations, the researchers focused on an RNA-editing enzyme called “TadA” that evolves into a DNA-editing enzyme. This conversion then makes it useful as precursor for adenine base editors (ABEs): when TadA is paired with a DNA-binding module, the resulting ABE is able to convert adenine (“A”) nucleobases into guanine (“G”) nucleobases. 

“Adenine that is being targeted is within the genome, which is within the nucleus, which, in turn, is within the cell,” explained Kartik Rallapalli, a Ph.D. student at UC San Diego who worked on the research alongside two professors, in an interview with UCSD’s Cynthia Dillon. “Hence, what we are targeting is very tightly guarded. Nature never bothered to have enzymes that could go in there and change things.”

The problem: enzymes like TadA are in short supply. So in an effort to find out what makes TadA tick, the researchers used their simulations to delve into the process that transforms TadA into a DNA-editing enzyme at an extremely granular level. To run those simulations, they turned to Comet, a supercomputer housed by the San Diego Supercomputer Center (SDSC). Comet’s 1944 Intel Haswell-based nodes and 72 Nvidia-based GPU nodes deliver 2.76 peak petaflops.

“The overarching goal of our study is to understand how evolution works in general—how evolutionary changes at the molecular level can train an existing enzyme to do something completely novel,”Rallapalli said. “By gathering atomistic insights into the process, we may be able to learn the rules of the evolutionary game and try to get ahead of natural evolution – try to convert more RNA-editing enzymes into DNA-editing enzymes, which can become novel genome editors.”

Specifically, the researchers examined the relationship between amino acid changes in the enzyme and its DNA-editing abilities. In another study, one of the researchers – Alexis Komor, an assistant professor at UC San Diego – had tested a series of amino acid changes to TadA, building a library of successfully evolved variants. 

“Given the stochastic nature of the evolutionary process that we employed, we had absolutely no idea of how these variants were working,” said Komor. “It’s really hard to study these enzymes inside a cell or even in a test tube. That’s where Kartik came in and provided us with an atomistic understanding of how particular amino acid changes in TadA enable this enzyme to do its chemistry on DNA.”

The researchers are hopeful that this research will help researchers narrow in on the most promising mechanisms for forcing that DNA-editing evolution, pushing genetic editing forward.

“These atomistic insights can focus our actual experimental efforts on certain amino acids, which can significantly reduce the cost and the labor of research and increase our chances of success,” Komor said. “We are thrilled to see what more this combination of simulations and experiments can reveal in the future.”

To read the UC San Diego article about this research, click here.

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industy updates delivered to you every week!

GigaIO Gets $14.7M in Series B Funding to Expand Its Composable Fabric Technology to Customers

September 16, 2021

Just before the COVID-19 pandemic began in March 2020, GigaIO introduced its Universal Composable Fabric technology, which allows enterprises to bring together any HPC and AI resources and integrate them with networking, Read more…

What’s New in HPC Research: Solar Power, ExaWorks, Optane & More

September 16, 2021

In this regular feature, HPCwire highlights newly published research in the high-performance computing community and related domains. From parallel programming to exascale to quantum computing, the details are here. Read more…

Cerebras Brings Its Wafer-Scale Engine AI System to the Cloud

September 16, 2021

Five months ago, when Cerebras Systems debuted its second-generation wafer-scale silicon system (CS-2), co-founder and CEO Andrew Feldman hinted of the company’s coming cloud plans, and now those plans have come to fruition. Today, Cerebras and Cirrascale Cloud Services are launching... Read more…

AI Hardware Summit: Panel on Memory Looks Forward

September 15, 2021

What will system memory look like in five years? Good question. While Monday's panel, Designing AI Super-Chips at the Speed of Memory, at the AI Hardware Summit, tackled several topics, the panelists also took a brief glimpse into the future. Unlike compute, storage and networking, which... Read more…

ECMWF Opens Bologna Datacenter in Preparation for Atos Supercomputer

September 14, 2021

In January 2020, the European Centre for Medium-Range Weather Forecasts (ECMWF) – a juggernaut in the weather forecasting scene – signed a four-year, $89-million contract with European tech firm Atos to quintuple its supercomputing capacity. With the deal approaching the two-year mark, ECMWF... Read more…

AWS Solution Channel

Supporting Climate Model Simulations to Accelerate Climate Science

The Amazon Sustainability Data Initiative (ASDI), AWS is donating cloud resources, technical support, and access to scalable infrastructure and fast networking providing high performance computing (HPC) solutions to support simulations of near-term climate using the National Center for Atmospheric Research (NCAR) Community Earth System Model Version 2 (CESM2) and its Whole Atmosphere Community Climate Model (WACCM). Read more…

Quantum Computer Market Headed to $830M in 2024

September 13, 2021

What is one to make of the quantum computing market? Energized (lots of funding) but still chaotic and advancing in unpredictable ways (e.g. competing qubit technologies), the quantum computing landscape is transforming Read more…

Cerebras Brings Its Wafer-Scale Engine AI System to the Cloud

September 16, 2021

Five months ago, when Cerebras Systems debuted its second-generation wafer-scale silicon system (CS-2), co-founder and CEO Andrew Feldman hinted of the company’s coming cloud plans, and now those plans have come to fruition. Today, Cerebras and Cirrascale Cloud Services are launching... Read more…

AI Hardware Summit: Panel on Memory Looks Forward

September 15, 2021

What will system memory look like in five years? Good question. While Monday's panel, Designing AI Super-Chips at the Speed of Memory, at the AI Hardware Summit, tackled several topics, the panelists also took a brief glimpse into the future. Unlike compute, storage and networking, which... Read more…

ECMWF Opens Bologna Datacenter in Preparation for Atos Supercomputer

September 14, 2021

In January 2020, the European Centre for Medium-Range Weather Forecasts (ECMWF) – a juggernaut in the weather forecasting scene – signed a four-year, $89-million contract with European tech firm Atos to quintuple its supercomputing capacity. With the deal approaching the two-year mark, ECMWF... Read more…

Quantum Computer Market Headed to $830M in 2024

September 13, 2021

What is one to make of the quantum computing market? Energized (lots of funding) but still chaotic and advancing in unpredictable ways (e.g. competing qubit tec Read more…

Amazon, NCAR, SilverLining Team for Unprecedented Cloud Climate Simulations

September 10, 2021

Earth’s climate is, to put it mildly, not in a good place. In the wake of a damning report from the Intergovernmental Panel on Climate Change (IPCC), scientis Read more…

After Roadblocks and Renewals, EuroHPC Targets a Bigger, Quantum Future

September 9, 2021

The EuroHPC Joint Undertaking (JU) was formalized in 2018, beginning a new era of European supercomputing that began to bear fruit this year with the launch of several of the first EuroHPC systems. The undertaking, however, has not been without its speed bumps, and the Union faces an uphill... Read more…

How Argonne Is Preparing for Exascale in 2022

September 8, 2021

Additional details came to light on Argonne National Laboratory’s preparation for the 2022 Aurora exascale-class supercomputer, during the HPC User Forum, held virtually this week on account of pandemic. Exascale Computing Project director Doug Kothe reviewed some of the 'early exascale hardware' at Argonne, Oak Ridge and NERSC (Perlmutter), while Ti Leggett, Deputy Project Director & Deputy Director... Read more…

IBM Introduces its First Power10-based Server, the Power E1080; Targets Hybrid Cloud

September 8, 2021

IBM today introduced the Power E1080 server, its first system powered by a Power10 IBM microprocessor. The new system reinforces IBM’s emphasis on hybrid cloud markets and the new chip beefs up its inference capabilities. IBM – like other CPU makers – is hoping to make inferencing a core capability... Read more…

Ahead of ‘Dojo,’ Tesla Reveals Its Massive Precursor Supercomputer

June 22, 2021

In spring 2019, Tesla made cryptic reference to a project called Dojo, a “super-powerful training computer” for video data processing. Then, in summer 2020, Tesla CEO Elon Musk tweeted: “Tesla is developing a [neural network] training computer called Dojo to process truly vast amounts of video data. It’s a beast! … A truly useful exaflop at de facto FP32.” Read more…

Berkeley Lab Debuts Perlmutter, World’s Fastest AI Supercomputer

May 27, 2021

A ribbon-cutting ceremony held virtually at Berkeley Lab's National Energy Research Scientific Computing Center (NERSC) today marked the official launch of Perlmutter – aka NERSC-9 – the GPU-accelerated supercomputer built by HPE in partnership with Nvidia and AMD. Read more…

Google Launches TPU v4 AI Chips

May 20, 2021

Google CEO Sundar Pichai spoke for only one minute and 42 seconds about the company’s latest TPU v4 Tensor Processing Units during his keynote at the Google I Read more…

Esperanto, Silicon in Hand, Champions the Efficiency of Its 1,092-Core RISC-V Chip

August 27, 2021

Esperanto Technologies made waves last December when it announced ET-SoC-1, a new RISC-V-based chip aimed at machine learning that packed nearly 1,100 cores onto a package small enough to fit six times over on a single PCIe card. Now, Esperanto is back, silicon in-hand and taking aim... Read more…

Enter Dojo: Tesla Reveals Design for Modular Supercomputer & D1 Chip

August 20, 2021

Two months ago, Tesla revealed a massive GPU cluster that it said was “roughly the number five supercomputer in the world,” and which was just a precursor to Tesla’s real supercomputing moonshot: the long-rumored, little-detailed Dojo system. “We’ve been scaling our neural network training compute dramatically over the last few years,” said Milan Kovac, Tesla’s director of autopilot engineering. Read more…

CentOS Replacement Rocky Linux Is Now in GA and Under Independent Control

June 21, 2021

The Rocky Enterprise Software Foundation (RESF) is announcing the general availability of Rocky Linux, release 8.4, designed as a drop-in replacement for the soon-to-be discontinued CentOS. The GA release is launching six-and-a-half months after Red Hat deprecated its support for the widely popular, free CentOS server operating system. The Rocky Linux development effort... Read more…

Intel Completes LLVM Adoption; Will End Updates to Classic C/C++ Compilers in Future

August 10, 2021

Intel reported in a blog this week that its adoption of the open source LLVM architecture for Intel’s C/C++ compiler is complete. The transition is part of In Read more…

Iran Gains HPC Capabilities with Launch of ‘Simorgh’ Supercomputer

May 18, 2021

Iran is said to be developing domestic supercomputing technology to advance the processing of scientific, economic, political and military data, and to strengthen the nation’s position in the age of AI and big data. On Sunday, Iran unveiled the Simorgh supercomputer, which will deliver.... Read more…

Leading Solution Providers

Contributors

AMD-Xilinx Deal Gains UK, EU Approvals — China’s Decision Still Pending

July 1, 2021

AMD’s planned acquisition of FPGA maker Xilinx is now in the hands of Chinese regulators after needed antitrust approvals for the $35 billion deal were receiv Read more…

Hot Chips: Here Come the DPUs and IPUs from Arm, Nvidia and Intel

August 25, 2021

The emergence of data processing units (DPU) and infrastructure processing units (IPU) as potentially important pieces in cloud and datacenter architectures was Read more…

10nm, 7nm, 5nm…. Should the Chip Nanometer Metric Be Replaced?

June 1, 2020

The biggest cool factor in server chips is the nanometer. AMD beating Intel to a CPU built on a 7nm process node* – with 5nm and 3nm on the way – has been i Read more…

Julia Update: Adoption Keeps Climbing; Is It a Python Challenger?

January 13, 2021

The rapid adoption of Julia, the open source, high level programing language with roots at MIT, shows no sign of slowing according to data from Julialang.org. I Read more…

HPE Wins $2B GreenLake HPC-as-a-Service Deal with NSA

September 1, 2021

In the heated, oft-contentious, government IT space, HPE has won a massive $2 billion contract to provide HPC and AI services to the United States’ National Security Agency (NSA). Following on the heels of the now-canceled $10 billion JEDI contract (reissued as JWCC) and a $10 billion... Read more…

Intel Launches 10nm ‘Ice Lake’ Datacenter CPU with Up to 40 Cores

April 6, 2021

The wait is over. Today Intel officially launched its 10nm datacenter CPU, the third-generation Intel Xeon Scalable processor, codenamed Ice Lake. With up to 40 Read more…

Quantum Roundup: IBM, Rigetti, Phasecraft, Oxford QC, China, and More

July 13, 2021

IBM yesterday announced a proof for a quantum ML algorithm. A week ago, it unveiled a new topology for its quantum processors. Last Friday, the Technical Univer Read more…

Frontier to Meet 20MW Exascale Power Target Set by DARPA in 2008

July 14, 2021

After more than a decade of planning, the United States’ first exascale computer, Frontier, is set to arrive at Oak Ridge National Laboratory (ORNL) later this year. Crossing this “1,000x” horizon required overcoming four major challenges: power demand, reliability, extreme parallelism and data movement. Read more…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire