While most people think about microscopy as involving light and lenses, a new type of microscopy based on DNA sequencing is quickly being developed. DNA microscopy involves knowing the relative positions of individual DNA molecules, due to diffusion and adjacency. Because DNA sequencing technologies are so powerful, giant networks of connections can be generated, allowing images with exquisitely fine structures to be realized. It’s as though a map was created from a set of directions (turn right here, then turn left and go fifty feet), rather than from an overarching view. Alex Boulgakov, a graduate student in Ed Marcotte’s lab, has been working on one such method, which was recently published in a preprint in bioRxiv [1].
News
Ellington Receives Research Foundation’s STAR Award
On July 12, 2019, Dr. Ellington received the Research Corporation for Science Advancement’s (RCSA) STAR award for his work on entrepreneurial education. In partnership with Dr. Sarah Eichhorn and the Texas Institute for Discovery Education, Dr. Ellington has helped to establish the Inventors’ Program, where students can take on translational problems and learn business-ready skills. As an example, Simren Lakhotia, an undergraduate researcher in the program, has worked on the development of a portable field diagnostic for Rocky Mountain spotted fever that would allow hikers to test individual ticks for the disease. Dr. Ellington was originally a Cottrell Scholar, an award that allowed teaching and research to be melded, and has since maintained a long association with the Research Foundation, an organization devoted to advancing science education.
Speeding Up Evolution using Artificial Intelligence
By Shaharyar Lakhani
An artificial neural network, a computer system modeled on the human neural system, allows a computer to figure out what constitutes a particular subject on its own. A research team in the Ellington Lab at the University of Texas at Austin is using this concept to recognize the ‘amino acid-ness’ of individual amino acids in a protein structure. They call the project “JMBLYA” because like the dish, they mix various components together to make a final product, in this case the mutated amino acids to make a protein. Various tests of JMBLYA have now proven it to be a time machine of sorts, where it can predict the future evolution of a protein to be more stable, and allows us to intervene in the present to make the beneficial mutation.
A New Biological and Financial Ecosystem for Plastic
By Shaharyar Lakhani
Plastics have been in popular use for only around 50 years, yet they have managed to saturate the planet. The toxic pollutants in plastics, combined with the long time they take to degrade, have adversely affected land, water, and air pollution. Nearly 300 million tons of plastic are produced every year, with the majority going to waste and ending up in landfills or the ocean. If the current trend continues, by 2050, the total weight of plastic in the ocean will be more than that of fish! But what if there was a way to turn this plastic into something positive? To have its pervasive presence in the ecosystem actually be a functioning part of that ecosystem?
‘Malice Analysis’ workshop held by Engineering Biology Research Consortium (EBRC) to Emphasize Biosecurity
By Shaharyar Lakhani
In order to build community awareness of risk and threat, the Engineering Biology Research Consortium (EBRC) held a “Malice Analysis Workshop” on Wednesday, June 19th. The workshop was sponsored by the Center for Systems and Synthetic Biology at the University of Texas at Austin. The objective of the workshop was to help researchers “identify potentially malicious applications of various projects, mitigation options, and what to do if you identify something and don’t know how to proceed.”
Intrinsically disordered regions regulate both catalytic and non-catalytic activities of the MutLα mismatch repair complex
From a publication in Oxford Academic
Intrinsically disordered regions (IDRs) are present in at least 30% of the eukaryotic proteome and are enriched in chromatin-associated proteins. Using a combination of genetics, biochemistry and single-molecule biophysics, we characterize how IDRs regulate the functions of the yeast MutLα (Mlh1–Pms1) mismatch repair (MMR) complex.
Changing the Genetic Code to Improve Biomedicine
By Shaharyar Lakhani
Along with most medical conditions come the high costs of pills and tablets. Even for everyday problems like headaches or pain, people tend to take an Aspirin or Tylenol. Many of these medications have to be taken in large doses or quite frequently in order to produce an effect. This is because the body tends to break down the bonds in these medicines easily. Resultantly, more money is spent on these medications. However, a group of researchers in the Ellington Lab led by Dr. Ross Thyer have found a solution to this problem. Normally, these medications have a dicysteine bond, which is easily broken down in the body. Dr. Thyer and his team replaced the sulfur atom of cysteine with the element immediately below it in the Periodic Table, selenium, which made the bond stronger and longer-lasting in the body, thus increasing the effect and decreasing the dosage.
Two UT Scientists Helping to Detect ‘Life As We Don’t Know It’
From an article posted on UT News
Two University of Texas at Austin faculty members have joined an interdisciplinary scientific team that is working with NASA to research new approaches to detecting extraterrestrial life. The UT Austin team will receive more than $722,000 over five years for the NASA project, which aims to develop methods to detect life on other worlds that might look nothing like life on Earth.
Ellington on the Industrialization of Biology
From an article published in ACS Synthetic Biology:
CSSB’s Andrew Ellington and co-author Douglas C. Friedman discuss the rise of bio-tech and its economic implications.
CSSB’s Ellington part of $4M UT-Austin BRAIN initiative grant
By Marc Airhart
Researchers at The University of Texas at Austin will receive three grants totaling $4 million to develop techniques for imaging and manipulating the activity of neurons in the brain, research that will help scientists explore the mechanisms of addiction, obesity, fear and many other brain states and disorders. The funding, provided by the National Institutes of Health, is part of the Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative launched last year by President Barack Obama.