Their work, which is described in the journal Physical Review E, provides an additional tool for understanding how biological systems function and could enhance methods and designs of technologies used in cancer and genetics research.
Biology researchers seek to measure cell activity, but the task is a challenging one because of its complexity—a cell has so many facets, all taking place simultaneously, that it is difficult to measure the behavior of its individual parts. Genes that do not necessarily affect each other inside a cell can disturb each others' measurements in a biotechnology device.
To get around these obstacles, the NYU researchers focused on how a cell's most basic components are measured—its DNA and RNA. Specifically, they used a cell's gene expressions as a "tagging system" to monitor cell behavior at its most fundamental level.
For this purpose, they focused on microarray technology in which researchers first gather data on the make-up of RNA molecules in two steps: RNA is first converted into cDNA, or "copy DNA," and then measured by hybridization.
However, the researchers' initial work involved not experiments, but, rather, the creation of mathematical models to predict "DNA-cDNA duplex formation." They developed an algebraic computation that allowed them to model arbitrary DNA-cDNA duplex formation, and, with it, measurements of cellular behavior. Specifically, they assigned to various chemical properties of DNA strands different algebraic values (e.g., "K," "X," "Y"). They then ran a series of computations that resulted in expressing how "matches" or "mismatches" among various strands of DNA can be characterized by the input algebraic variables. These computations could then be used directly to design the most accurate biotechnology for measuring cellular behavior.
To confirm the validity of these algebraic models, the researchers conducted laboratory experiments involving the hybridization of DNA sequences. These results largely confirmed those predicted by the mathematical models—the DNA sequences in the laboratory matched up in most instances in ways the models forecast.
The study's co-authors were: Vera Cherepinsky, a former post-doctoral fellow at NYU's Courant Institute of Mathematical Sciences and currently in the Department of Mathematics and Computer Science at Fairfield University; Ghazala Hashmi of BioArray Solutions, Ltd.; and Bud Mishra, a professor of computer science and mathematics and a principal investigator in Courant Bioinformatics Group.
James Devitt | EurekAlert!
Astronomers find unexpected, dust-obscured star formation in distant galaxy
24.03.2017 | University of Massachusetts at Amherst
Gravitational wave kicks monster black hole out of galactic core
24.03.2017 | NASA/Goddard Space Flight Center
Astronomers from Bonn and Tautenburg in Thuringia (Germany) used the 100-m radio telescope at Effelsberg to observe several galaxy clusters. At the edges of these large accumulations of dark matter, stellar systems (galaxies), hot gas, and charged particles, they found magnetic fields that are exceptionally ordered over distances of many million light years. This makes them the most extended magnetic fields in the universe known so far.
The results will be published on March 22 in the journal „Astronomy & Astrophysics“.
Galaxy clusters are the largest gravitationally bound structures in the universe. With a typical extent of about 10 million light years, i.e. 100 times the...
Researchers at the Goethe University Frankfurt, together with partners from the University of Tübingen in Germany and Queen Mary University as well as Francis Crick Institute from London (UK) have developed a novel technology to decipher the secret ubiquitin code.
Ubiquitin is a small protein that can be linked to other cellular proteins, thereby controlling and modulating their functions. The attachment occurs in many...
In the eternal search for next generation high-efficiency solar cells and LEDs, scientists at Los Alamos National Laboratory and their partners are creating...
Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are less stable. Now researchers at the Technical University of Munich (TUM) have, for the first time ever, produced a composite material combining silicon nanosheets and a polymer that is both UV-resistant and easy to process. This brings the scientists a significant step closer to industrial applications like flexible displays and photosensors.
Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are...
Enzymes behave differently in a test tube compared with the molecular scrum of a living cell. Chemists from the University of Basel have now been able to simulate these confined natural conditions in artificial vesicles for the first time. As reported in the academic journal Small, the results are offering better insight into the development of nanoreactors and artificial organelles.
Enzymes behave differently in a test tube compared with the molecular scrum of a living cell. Chemists from the University of Basel have now been able to...
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