Category Archives: BioEngineering

Fort Worth Star Telegram

UTA raises cancer research profile with $6 million in grants Fort Worth Star Telegram UTA has more than 25 cancer researchers in its biology, bioengineering and computer science colleges and has 13 cancer-related patents issued in the past five years. Last year, UTA joined the ranks of top research universities listed by the Carnegie ...

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UTA raises cancer research profile with $6 million in grants - Fort Worth Star Telegram

Lifeboat Foundation

Computing with biochemical circuits made easy -- ScienceDaily Science Daily A software tool and a systematic wet-lab procedure proven in practice are an advance in the design and construction of circuits made of DNA. Computing with biochemical circuits made easy - Lifeboat News ...Lifeboat Foundation (blog) all 2 news articles »

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Computing with biochemical circuits made easy -- ScienceDaily - Science Daily

February 24, 2017 Artistic rendering of RNA-DNA interactions. A 3-D structure of tightly coiled DNA is depicted as the body of a dragon in Chinese myth. Interacting RNAs are depicted as hairs, whiskers and claws, which are essential for the dragon to function. Credit: Victor O. Leshyk

Bioengineers at the University of California San Diego have developed a new tool to identify interactions between RNA and DNA molecules. The tool, called MARGI (Mapping RNA Genome Interactions), is the first technology that's capable of providing a full account of all the RNA molecules that interact with a segment of DNA, as well as the locations of all these interactionsin just a single experiment.

RNA molecules can attach to particular DNA sequences to help control how much protein these particular genes produce within a given time, and within a given cell. And by knowing what genes produce these regulatory RNAs, researchers can start to identify new functions and instructions encoded in the genome.

"Most of the human genome sequence is now known, but we still don't know what most of these sequences mean," said Sheng Zhong, bioengineering professor at the UC San Diego Jacobs School of Engineering and the study's lead author. "To better understand the functions of the genome, it would be useful to have the entire catalog of all the RNA molecules that interact with DNA, and what sequences they interact with. We've developed a tool that can give us that information."

Zhong and his team published their findings in the Feb. issue of Current Biology.

Existing methods to study RNA-DNA interactions are only capable of analyzing one RNA molecule at a time, making it impossible to analyze an entire set of RNA-DNA interactions involving hundreds of RNA molecules.

"It could take years to analyze all these interactions," said Tri Nguyen, a bioengineering Ph.D. student at UC San Diego and a co-first author of the study.

Using MARGI, an entire set of RNA-DNA interactions could be analyzed in a single experiment that takes one to two weeks.

The MARGI technique starts out with a mixture containing DNA that's been cut into short pieces and RNA. In this mixture, a subset of RNA molecules are interacting with particular DNA pieces. A specially designed linker is then added to connect the interacting RNA-DNA pairs. Linked RNA-DNA pairs are selectively fished out, then converted into chimeric sequences that can all be read at once using high-throughput sequencing.

Zhong and his team tested the method's accuracy by seeing if it produced false positive results. First, the researchers mixed RNA and DNA from both fruit fly and human cells, creating both "true" RNA-DNA pairs, meaning they're either fully human or fully fruit fly, and "false" RNA-DNA pairs, meaning they're half human and half fruit flythese are the ones that shouldn't be detected. The team then screened the entire mixture using MARGI. The method detected a large set of true RNA-DNA interactions, but it also detected approximately 2 percent of the false ones.

"This method is not perfect, but it's an important step toward creating a full functional annotation of the genome," said co-first author Bharat Sridhar, a visiting bioengineering researcher in Zhong's group.

Explore further: Size matters... and structure too: New tool predicts the interaction of proteins with long non-coding RNAs

More information: Bharat Sridhar et al, Systematic Mapping of RNA-Chromatin Interactions InVivo, Current Biology (2017). DOI: 10.1016/j.cub.2017.01.011

Far from just reading the information contained in the human genome, and in order to fully understand how it works, researchers aim to know the ins and outs of all the elements in this tiny regulated gear. Many laboratories, ...

Every cell has its own individual molecular fingerprint, which is informative for its functions and regulatory states. LMU researchers have now carried out a comprehensive comparison of methodologies that quantify RNAs of ...

After the 2003 completion of the Human Genome Project which sequenced all 3 billion "letters," or base pairs, in the human genome many thought that our DNA would become an open book. But a perplexing problem quickly ...

What used to be dismissed by many as "junk DNA" is back with a vengeance as growing data points to the importance of non-coding RNAs (ncRNAs)genome's messages that do not code for proteinsin development and disease. ...

An algorithm which models how proteins inside cells interact with each other will enhance the study of biology, and sheds light on how proteins work together to complete tasks such as turning food into energy.

Since the completion of the human genome an important goal has been to elucidate the function of the now known proteins: a new molecular method enables the investigation of the function for thousands of proteins in parallel. ...

Photographers, poachers and eco-tour operators are in the crosshairs of a Canadian conservationist who warns that tracking tags are being hacked and misused to harass and hunt endangered animals.

Bioengineers at the University of California San Diego have developed a new tool to identify interactions between RNA and DNA molecules. The tool, called MARGI (Mapping RNA Genome Interactions), is the first technology that's ...

Small "bubbles" frequently form on membranes of cells and are taken up into their interior. The process involves EHD proteins - a focus of research by Prof. Oliver Daumke of the MDC. He and his team have now shed light on ...

The first skirmish was fought last week in what could be a long war over a revolutionary patent on gene-editing technology, with colossal amounts of money at stake.

Scientists from The University of Western Australia have identified a tiny mutation in plants that can influence how well a plant recovers from stressful conditions, and ultimately impact a plant's survival.

The last Neanderthal died 40,000 years ago, but much of their genome lives on, in bits and pieces, through modern humans. The impact of Neanderthals' genetic contribution has been uncertain: Do these snippets affect our genome's ...

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New tool to map RNA-DNA interactions could help researchers ... - Phys.Org

Newswise Researchers in bioengineering at the University of Notre Dame will join a consortium of academia, industry and government organizations and the nonprofit sector to develop next-generation manufacturing processes and technologies for cells, tissues and organs.

The Advanced Regenerative Manufacturing Institute (ARMI), Manufacturing USA initiative, will bring together close to 100 partner organizations as part of continuing efforts to help revitalize American manufacturing and incentivize companies to invest in new technology development in the United States. Approximately $80 million from the Department of Defense will be combined with more than $200 million in cost share to support the development of tissue and organ manufacturing capabilities.

Scientists at Notre Dame will focus on the challenges of advanced tissue biofabrication, as well as making current technologies and solutions available to patients in need. As part of the consortium, the university joins 47 industrial partners, 26 academic and academically affiliated partners, and 14 government and nonprofit partners. The ARMI will focus on accelerating regenerative tissue research and creating state-of-the-art manufacturing innovations in biomaterial and cell processing for critical Department of Defense and civilian needs.

Notre Dame researchers and bioengineers already direct several federally funded research programs in regenerative medicine through the colleges of science and engineering and in conjunction with the Notre Dame Center for Stem Cells and Regenerative Medicine.

Were looking forward to collaborating with this group of industrial and academic partners, said Glen Niebur, professor of aerospace and mechanical engineering and director of the bioengineering graduate program at Notre Dame. Through our affiliation with ARMI, we have a great opportunity to contribute to making regenerative medicine products a reality.

The ARMI marks the third Manufacturing USA institute that the university has partnered with, including LIFT (Lightweight Innovations for Tomorrow) and the Digital Manufacturing & Design Innovation Institute.

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University of Notre Dame Partners with the Advanced Regenerative Manufacturing Institute - Newswise (press release)

Expanding biomedical engineering programs could boost state's life ... MiBiz As Michigan life sciences companies grow and seek to commercialize their innovations, the firms often face key constraints when it comes to access to capital in ... and more »

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Expanding biomedical engineering programs could boost state's life ... - MiBiz

The human species is about to change dramatically. That's the argument Yuval Noah Harari makes in his new book, Homo Deus: A Brief History of Tomorrow.

Harari is a history professor at Hebrew University in Israel. He tells NPR's Ari Shapiro that he expects we will soon engineer our bodies and minds in the same way we now design products.

On how we will begin to engineer bodies

The three main ways of doing that, first of all, is to take our organic body and start tinkering with it with things like genetic engineering, speeding up natural selection and actually replacing it with intelligent design not the intelligent design of some God above the clouds, but our intelligent design.

The other way is to start combining organic with inorganic parts and creating cyborgs. For four billion years all of evolution not just of humans but of all beings was confined to the organic realm, but very soon we might be able to break out of the organic realm using things like brain-computer interfaces, which combine organic parts like an organic brain with inorganic parts like bionic hands or eyes or ears.

And then the third and most extreme path is to create completely inorganic beings not even needing an organic brain, but using instead artificial intelligence.

On one way a future medical breakthrough could be used to upgrade a healthy person

I think in general medicine in the 21st century will switch from healing the sick to upgrading the healthy. ... If you find ways to repair the memory damaged by Alzheimer's disease or dementia and so forth, it is very likely that the same methods could be used to upgrade the memory of completely healthy people. And if you find ways to connect brains and computers, you can rely on memory's immense databases outside your own brain. We are starting to do it, in a way, with our smart phones and computers, but what we may see in coming decades is humans actually merging completely with their smart phones and computers.

On biological inequality

It's likely that all the upgrades, at least at first, will cost a lot and will be available only to a small elite. So for the first time in human history we might see economic inequality being translated into biological inequality. And once such a gate opens, it becomes almost impossible to close it because then the rich will really be far more capable than everybody else.

On what can be done to control the growth of bioengineering and artificial intelligence

One thing that we need to do is start thinking far more seriously about global governance because the only solution to such problems will be on a global level, not on a national level.

Actually, of course, in the last year or two we are seeing a retrograde movement away from globalist thinking and into more nationalist and isolationist thinking, and this is very dangerous. I mean, traditionally, people said that nationalism is dangerous because it leads to war. But now nationalism is far more dangerous because not only it leads to war, it also may prevent us from having any effective answer that can help us cope with dangers like the rise of artificial intelligence or the implications of bioengineering.

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Are Cyborgs In Our Future? 'Homo Deus' Author Thinks So - NPR