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News Article | November 24, 2016
Site: phys.org

Molecules with silicon-carbon, or organosilicon, compounds are found in pharmaceuticals as well as in many other products, including agricultural chemicals, paints, semiconductors, and computer and TV screens. Currently, these products are made synthetically, since the silicon-carbon bonds are not found in nature. The new study demonstrates that biology can instead be used to manufacture these bonds in ways that are more environmentally friendly and potentially much less expensive. "We decided to get nature to do what only chemists could do—only better," says Frances Arnold, Caltech's Dick and Barbara Dickinson Professor of Chemical Engineering, Bioengineering and Biochemistry, and principal investigator of the new research, published in the Nov. 24 issue of the journal Science. The study is also the first to show that nature can adapt to incorporate silicon into carbon-based molecules, the building blocks of life. Scientists have long wondered if life on Earth could have evolved to be based on silicon instead of carbon. Science-fiction authors likewise have imagined alien worlds with silicon-based life, like the lumpy Horta creatures portrayed in an episode of the 1960s TV series Star Trek. Carbon and silicon are chemically very similar. They both can form bonds to four atoms simultaneously, making them well suited to form the long chains of molecules found in life, such as proteins and DNA. "No living organism is known to put silicon-carbon bonds together, even though silicon is so abundant, all around us, in rocks and all over the beach," says Jennifer Kan, a postdoctoral scholar in Arnold's lab and lead author of the new study. Silicon is the second most abundant element in Earth's crust. The researchers used a method called directed evolution, pioneered by Arnold in the early 1990s, in which new and better enzymes are created in labs by artificial selection, similar to the way that breeders modify corn, cows, or cats. Enzymes are a class of proteins that catalyze, or facilitate, chemical reactions. The directed evolution process begins with an enzyme that scientists want to enhance. The DNA coding for the enzyme is mutated in more-or-less random ways, and the resulting enzymes are tested for a desired trait. The top-performing enzyme is then mutated again, and the process is repeated until an enzyme that performs much better than the original is created. Directed evolution has been used for years to make enzymes for household products, like detergents; and for "green" sustainable routes to making pharmaceuticals, agricultural chemicals, and fuels. In the new study, the goal was not just to improve an enzyme's biological function but to actually persuade it to do something that it had not done before. The researchers' first step was to find a suitable candidate, an enzyme showing potential for making the silicon-carbon bonds. "It's like breeding a racehorse," says Arnold, who is also the director of the Donna and Benjamin M. Rosen Bioengineering Center at Caltech. "A good breeder recognizes the inherent ability of a horse to become a racer and has to bring that out in successive generations. We just do it with proteins." The ideal candidate turned out to be a protein from a bacterium that grows in hot springs in Iceland. That protein, called cytochrome c, normally shuttles electrons to other proteins, but the researchers found that it also happens to act like an enzyme to create silicon-carbon bonds at low levels. The scientists then mutated the DNA coding for that protein within a region that specifies an iron-containing portion of the protein thought to be responsible for its silicon-carbon bond-forming activity. Next, they tested these mutant enzymes for their ability to make organosilicon compounds better than the original. After only three rounds, they had created an enzyme that can selectively make silicon-carbon bonds 15 times more efficiently than the best catalyst invented by chemists. Furthermore, the enzyme is highly selective, which means that it makes fewer unwanted byproducts that have to be chemically separated out. "This iron-based, genetically encoded catalyst is nontoxic, cheaper, and easier to modify compared to other catalysts used in chemical synthesis," says Kan. "The new reaction can also be done at room temperature and in water." The synthetic process for making silicon-carbon bonds often uses precious metals and toxic solvents, and requires extra processing to remove unwanted byproducts, all of which add to the cost of making these compounds. As to the question of whether life can evolve to use silicon on its own, Arnold says that is up to nature. "This study shows how quickly nature can adapt to new challenges," she says. "The DNA-encoded catalytic machinery of the cell can rapidly learn to promote new chemical reactions when we provide new reagents and the appropriate incentive in the form of artificial selection. Nature could have done this herself if she cared to." Explore further: Scientists replace iron in muscle protein with non-biological metal More information: Directed Evolution of Cytochrome c for Carbon-Silicon Bond Formation: Bringing Silicon to Life," Science, science.sciencemag.org/cgi/doi/10.1126/science.aah6219


News Article | November 24, 2016
Site: www.eurekalert.org

A new study is the first to show that living organisms can be persuaded to make silicon-carbon bonds--something only chemists had done before. Scientists at Caltech "bred" a bacterial protein to make the man-made bonds--a finding that has applications in several industries. Molecules with silicon-carbon, or organosilicon, compounds are found in pharmaceuticals as well as in many other products, including agricultural chemicals, paints, semiconductors, and computer and TV screens. Currently, these products are made synthetically, since the silicon-carbon bonds are not found in nature. The new study demonstrates that biology can instead be used to manufacture these bonds in ways that are more environmentally friendly and potentially much less expensive. "We decided to get nature to do what only chemists could do--only better," says Frances Arnold, Caltech's Dick and Barbara Dickinson Professor of Chemical Engineering, Bioengineering and Biochemistry, and principal investigator of the new research, published in the Nov. 24 issue of the journal Science. The study is also the first to show that nature can adapt to incorporate silicon into carbon-based molecules, the building blocks of life. Scientists have long wondered if life on Earth could have evolved to be based on silicon instead of carbon. Science-fiction authors likewise have imagined alien worlds with silicon-based life, like the lumpy Horta creatures portrayed in an episode of the 1960s TV series Star Trek. Carbon and silicon are chemically very similar. They both can form bonds to four atoms simultaneously, making them well suited to form the long chains of molecules found in life, such as proteins and DNA. "No living organism is known to put silicon-carbon bonds together, even though silicon is so abundant, all around us, in rocks and all over the beach," says Jennifer Kan, a postdoctoral scholar in Arnold's lab and lead author of the new study. Silicon is the second most abundant element in Earth's crust. The researchers used a method called directed evolution, pioneered by Arnold in the early 1990s, in which new and better enzymes are created in labs by artificial selection, similar to the way that breeders modify corn, cows, or cats. Enzymes are a class of proteins that catalyze, or facilitate, chemical reactions. The directed evolution process begins with an enzyme that scientists want to enhance. The DNA coding for the enzyme is mutated in more-or-less random ways, and the resulting enzymes are tested for a desired trait. The top-performing enzyme is then mutated again, and the process is repeated until an enzyme that performs much better than the original is created. Directed evolution has been used for years to make enzymes for household products, like detergents; and for "green" sustainable routes to making pharmaceuticals, agricultural chemicals, and fuels. In the new study, the goal was not just to improve an enzyme's biological function but to actually persuade it to do something that it had not done before. The researchers' first step was to find a suitable candidate, an enzyme showing potential for making the silicon-carbon bonds. "It's like breeding a racehorse," says Arnold, who is also the director of the Donna and Benjamin M. Rosen Bioengineering Center at Caltech. "A good breeder recognizes the inherent ability of a horse to become a racer and has to bring that out in successive generations. We just do it with proteins." The ideal candidate turned out to be a protein from a bacterium that grows in hot springs in Iceland. That protein, called cytochrome c, normally shuttles electrons to other proteins, but the researchers found that it also happens to act like an enzyme to create silicon-carbon bonds at low levels. The scientists then mutated the DNA coding for that protein within a region that specifies an iron-containing portion of the protein thought to be responsible for its silicon-carbon bond-forming activity. Next, they tested these mutant enzymes for their ability to make organosilicon compounds better than the original. After only three rounds, they had created an enzyme that can selectively make silicon-carbon bonds 15 times more efficiently than the best catalyst invented by chemists. Furthermore, the enzyme is highly selective, which means that it makes fewer unwanted byproducts that have to be chemically separated out. "This iron-based, genetically encoded catalyst is nontoxic, cheaper, and easier to modify compared to other catalysts used in chemical synthesis," says Kan. "The new reaction can also be done at room temperature and in water." The synthetic process for making silicon-carbon bonds often uses precious metals and toxic solvents, and requires extra processing to remove unwanted byproducts, all of which add to the cost of making these compounds. As to the question of whether life can evolve to use silicon on its own, Arnold says that is up to nature. "This study shows how quickly nature can adapt to new challenges," she says. "The DNA-encoded catalytic machinery of the cell can rapidly learn to promote new chemical reactions when we provide new reagents and the appropriate incentive in the form of artificial selection. Nature could have done this herself if she cared to." The Science paper, titled "Directed Evolution of Cytochrome c for Carbon-Silicon Bond Formation: Bringing Silicon to Life," is also authored by Russell Lewis and Kai Chen of Caltech. The research is funded by the National Science Foundation, the Caltech Innovation Initiative program, and the Jacobs Institute for Molecular Engineering for Medicine at Caltech.


News Article | November 28, 2016
Site: astrobiology.com

A new study is the first to show that living organisms can be persuaded to make silicon-carbon bonds--something only chemists had done before. Scientists at Caltech "bred" a bacterial protein to have the ability to make the man-made bonds, a finding that has applications in several industries. Molecules with silicon-carbon, or organosilicon, compounds are found in pharmaceuticals as well as in many other products, including agricultural chemicals, paints, semiconductors, and computer and TV screens. Currently, these products are made synthetically, since the silicon-carbon bonds are not found in nature. The new research, which recently won Caltech's Dow Sustainability Innovation Student Challenge Award (SISCA) grand prize, demonstrates that biology can instead be used to manufacture these bonds in ways that are more environmentally friendly and potentially much less expensive. "We decided to get nature to do what only chemists could do--only better," says Frances Arnold, Caltech's Dick and Barbara Dickinson Professor of Chemical Engineering, Bioengineering and Biochemistry, and principal investigator of the new research, published in the Nov. 24 issue of the journal Science. The study is also the first to show that nature can adapt to incorporate silicon into carbon-based molecules, the building blocks of life. Scientists have long wondered if life on Earth could have evolved to be based on silicon instead of carbon. Science-fiction authors likewise have imagined alien worlds with silicon-based life, like the lumpy Horta creatures portrayed in an episode of the 1960s TV series Star Trek. Carbon and silicon are chemically very similar. They both can form bonds to four atoms simultaneously, making them well suited to form the long chains of molecules found in life, such as proteins and DNA. "No living organism is known to put silicon-carbon bonds together, even though silicon is so abundant, all around us, in rocks and all over the beach," says Jennifer Kan, a postdoctoral scholar in Arnold's lab and lead author of the new study. Silicon is the second most abundant element in Earth's crust. The researchers used a method called directed evolution, pioneered by Arnold in the early 1990s, in which new and better enzymes are created in labs by artificial selection, similar to the way that breeders modify corn, cows, or cats. Enzymes are a class of proteins that catalyze, or facilitate, chemical reactions. The directed evolution process begins with an enzyme that scientists want to enhance. The DNA coding for the enzyme is mutated in more-or-less random ways, and the resulting enzymes are tested for a desired trait. The top-performing enzyme is then mutated again, and the process is repeated until an enzyme that performs much better than the original is created. Directed evolution has been used for years to make enzymes for household products, like detergents; and for "green" sustainable routes to making pharmaceuticals, agricultural chemicals, and fuels. In the new study, the goal was not just to improve an enzyme's biological function but to actually persuade it to do something that it had not done before. The researchers' first step was to find a suitable candidate, an enzyme showing potential for making the silicon-carbon bonds. "It's like breeding a racehorse," says Arnold, who is also the director of the Donna and Benjamin M. Rosen Bioengineering Center at Caltech. "A good breeder recognizes the inherent ability of a horse to become a racer and has to bring that out in successive generations. We just do it with proteins." The ideal candidate turned out to be a protein from a bacterium that grows in hot springs in Iceland. That protein, called cytochrome c, normally shuttles electrons to other proteins, but the researchers found that it also happens to act like an enzyme to create silicon-carbon bonds at low levels. The scientists then mutated the DNA coding for that protein within a region that specifies an iron-containing portion of the protein thought to be responsible for its silicon-carbon bond-forming activity. Next, they tested these mutant enzymes for their ability to make organosilicon compounds better than the original. After only three rounds, they had created an enzyme that can selectively make silicon-carbon bonds 15 times more efficiently than the best catalyst invented by chemists. Furthermore, the enzyme is highly selective, which means that it makes fewer unwanted byproducts that have to be chemically separated out. "This iron-based, genetically encoded catalyst is nontoxic, cheaper, and easier to modify compared to other catalysts used in chemical synthesis," says Kan. "The new reaction can also be done at room temperature and in water." The synthetic process for making silicon-carbon bonds often uses precious metals and toxic solvents, and requires extra processing to remove unwanted byproducts, all of which add to the cost of making these compounds. As to the question of whether life can evolve to use silicon on its own, Arnold says that is up to nature. "This study shows how quickly nature can adapt to new challenges," she says. "The DNA-encoded catalytic machinery of the cell can rapidly learn to promote new chemical reactions when we provide new reagents and the appropriate incentive in the form of artificial selection. Nature could have done this herself if she cared to." The Science paper, titled "Directed Evolution of Cytochrome c for Carbon-Silicon Bond Formation: Bringing Silicon to Life," is also authored by Russell Lewis and Kai Chen of Caltech. The research is funded by the National Science Foundation, the Caltech Innovation Initiative program, and the Jacobs Institute for Molecular Engineering for Medicine at Caltech.


Goryunova S.V.,Russian Academy of Sciences | Chikida N.N.,All Russian Institute of Plant Industry | Kochieva E.Z.,Bioengineering Center
Russian Journal of Genetics | Year: 2010

RAPD analysis was used to study the genetic variation and phylogenetic relationships of polyploid Aegilops species with the U genome. In total, 115 DNA samples of eight polyploid species containing the U genome and the diploid species Ae. umbellulata (U) were examined. Substantial interspecific polymorphism was observed for the majority of the polyploid species with the U genome (interspecific differences, 0. 01-0,2; proportion of polymorphic loci, 56. 6-88. 2%). Aegilops triuncialis was identified as the only alloploid species with low interspecific polymorphism (interspecific differences, 0-0. 01, P = 50%) in the U-genome group. The U-genome Aegilops species proved to be separated from other species of the genus. The phylogenetic relationships were established for the U-genome species. The greatest separation within the U-genome group was observed for the US-genome species Ae. kotschyi and Ae. variabilis. The tetraploid species Ae. triaristata and Ae. columnaris, which had the UX genome, and the hexaploid species Ae. recta (UXN) were found to be related to each other and separate from the UM-genome species. A similarity was observed between the UM-genome species Ae. ovata and Ae. biuncialis, which had the UM genome, and the ancestral diploid U-genome species Ae. umbellulata. The UC-genome species Ae. triuncialis was rather separate and slightly similar to the UX-genome species. © 2010 Pleiades Publishing, Ltd.


Luongo K.,Florida International University | Luongo K.,Bioengineering Center | Luongo K.,University of South Florida | Holton A.,Bioengineering Center | And 6 more authors.
Biomicrofluidics | Year: 2013

In this paper, we report the design, fabrication, and testing of a lab-on-a-chip based microfluidic device for application of trapping and measuring the dielectric properties of microtumors over time using electrical impedance spectroscopy (EIS). Microelectromechanical system (MEMS) techniques were used to embed opposing electrodes onto the top and bottom surfaces of a microfluidic channel fabricated using Pyrex substrate, chrome gold, SU-8, and polydimethylsiloxane. Differing concentrations of cell culture medium, differing sized polystyrene beads, and MCF-7 microtumor spheroids were used to validate the designs ability to detect background conductivity changes and dielectric particle diameter changes between electrodes. The observed changes in cell medium concentrations demonstrated a linear relation to extracted solution resistance (Rs), while polystyrene beads and multicell spheroids induced changes in magnitude consistent with diameter increase. This design permits optical correlation between electrical measurements and EIS spectra. © 2013 AIP Publishing LLC.


Golubkina N.,Russian Academy of Medical Sciences | Skriabin K.,Bioengineering Center
Journal of Food Composition and Analysis | Year: 2010

Although ordinary and genetically modified potatoes stable to Colorado beetles (CPB), Leptinotarsa decemlineata Say, are known to possess very small differences in chemical composition, nothing is known about selenium (Se) accumulation by these plants. Using a fluorimetric method of analysis, we have demonstrated extremely high Se accumulation in leaves of CPB-resistant potatoes (more than 1 mg kg -1 dry weight) and moderate accumulation levels of Se in tubers (1.39 times more than in ordinary plants). Leaves of genetically modified potatoes are shown to possess a decreased concentration of ascorbic acid (1.5 times less than controls) and slightly elevated levels of nitrates. The possibility of Se participation in the protection of genetically modified potatoes against CPB is discussed. © 2009 Elsevier Inc. All rights reserved.


Ushakova N.A.,RAS Severtsov Institute of Ecology | Abramov V.M.,Institute of Immunological Engineering | Khlebnikov V.S.,Institute of Immunological Engineering | Semenov A.M.,Moscow State University | And 8 more authors.
Probiotics and Antimicrobial Proteins | Year: 2012

The biofilm formation took place in 48 h within the solid substrate cultivation of Lactobacillus plantarum 8-RA-3 strain on the wheat bran saturated with the MRS medium. The drying of the bran fermented by lactobacilli resulted in a decrease in the number of colony-forming units (CFU) from 23. 0 × 10 8 to 6. 9 × 10 5 CFU/g in daily samples and to less than 10 4 CFU/g in 2- and 3-day samples. However, according to the fluorescence-based live/dead assay data, more than 40 % of the non-cultured bacteria were viable. As a result of mice kept on a diet with the introduction of bran fermented by Lact. plantarum 8-RA-3 for 72 h into the fodder, a recovery of normal level of intestinal lactobacilli, inhibited by administration of antibiotic was noted. The strain genetically identical to the Lact. plantarum 8-RA-3 was isolated from the feces of these mice. The results indicate that solid substrate cultivated Lact. plantarum 8-RA-3 strain formed a biofilm. Once dried and transferred into a non-cultured state, biofilm cells retained its viability and biological activity. © 2012 Springer Science + Business Media, LLC.


Zhu F.,Bioengineering Center | Kalra A.,Bioengineering Center | Saif T.,Bioengineering Center | Yang Z.,Boston College | And 2 more authors.
Computer Methods in Biomechanics and Biomedical Engineering | Year: 2015

Traumatic brain injury due to primary blast loading has become a signature injury in recent military conflicts and terrorist activities. Extensive experimental and computational investigations have been conducted to study the interrelationships between intracranial pressure response and intrinsic or ‘input’ parameters such as the head geometry and loading conditions. However, these relationships are very complicated and are usually implicit and ‘hidden’ in a large amount of simulation/test data. In this study, a data mining method is proposed to explore such underlying information from the numerical simulation results. The heads of different species are described as a highly simplified two-part (skull and brain) finite element model with varying geometric parameters. The parameters considered include peak incident pressure, skull thickness, brain radius and snout length. Their interrelationship and coupling effect are discovered by developing a decision tree based on the large simulation data-set. The results show that the proposed data-driven method is superior to the conventional linear regression method and is comparable to the nonlinear regression method. Considering its capability of exploring implicit information and the relatively simple relationships between response and input variables, the data mining method is considered to be a good tool for an in-depth understanding of the mechanisms of blast-induced brain injury. As a general method, this approach can also be applied to other nonlinear complex biomechanical systems. © 2015 Taylor & Francis


Goryunova S.V.,Wageningen University | Goryunova S.V.,Russian Academy of Sciences | Salentijn E.M.J.,Wageningen University | Chikida N.N.,All Russian Institute of Plant Industry | And 4 more authors.
BMC Evolutionary Biology | Year: 2012

Background: The gamma-gliadins are considered to be the oldest of the gliadin family of storage proteins in Aegilops/Triticum. However, the expansion of this multigene family has not been studied in an evolutionary perspective. Results: We have cloned 59 gamma-gliadin genes from Aegilops and Triticum species (Aegilops caudata L., Aegilops comosa Sm. in Sibth. & Sm., Aegilops mutica Boiss., Aegilops speltoides Tausch, Aegilops tauschii Coss., Aegilops umbellulata Zhuk., Aegilops uniaristata Vis., and Triticum monococcum L.) representing eight different genomes: A§ssup§m§esup§, B/S, C, D, M, N, T and U. Overall, 15% of the sequences contained internal stop codons resulting in pseudogenes, but this percentage was variable among genomes, up to over 50% in Ae. umbellulata. The most common length of the deduced protein, including the signal peptide, was 302 amino acids, but the length varied from 215 to 362 amino acids, both obtained from Ae. speltoides. Most genes encoded proteins with eight cysteines. However, all Aegilops species had genes that encoded a gamma-gliadin protein of 302 amino acids with an additional cysteine. These conserved nine-cysteine gamma-gliadins may perform a specific function, possibly as chain terminators in gluten network formation in protein bodies during endosperm development. A phylogenetic analysis of gamma-gliadins derived from Aegilops and Triticum species and the related genera Lophopyrum, Crithopsis, and Dasypyrum showed six groups of genes. Most Aegilops species contained gamma-gliadin genes from several of these groups, which also included sequences from the genera Lophopyrum, Crithopsis, and Dasypyrum. Hordein and secalin sequences formed separate groups. Conclusions: We present a model for the evolution of the gamma-gliadins from which we deduce that the most recent common ancestor (MRCA) of Aegilops/Triticum-Dasypyrum-Lophopyrum-Crithopsis already had four groups of gamma-gliadin sequences, presumably the result of two rounds of duplication of the locus. © 2012 Goryunova et al.; licensee BioMed Central Ltd.


Cuiffi J.,Bioengineering Center | Soong R.,Draper Laboratory | Manolakos S.,Bioengineering Center | Mohapatra S.,University of South Florida | Larson D.,Draper Laboratory
IFMBE Proceedings | Year: 2010

We present a review of current implementations of nanohole array sensor technology and discuss future trends for this technique applied to multiplexed, label-free protein binding assays. Nanohole array techniques are similar to surface plasmon resonance (SPR) techniques in that local refractive index changes at the sensor surface, correlated to protein binding events, are probed and detected optically. Nanohole array sensing differs by use of a transmission based mode of optical detection, extraordinary optical transmission (EOT) that eliminates the need for prism coupling to the surface and provides high spatial and temporal resolution for chip-based assays. This enables nanohole array sensor technology to combine the real time label-free analysis of SPR with the multiplexed assay format of protein microarrays. Various implementations and configurations of nanohole array sensing have been demonstrated, but the use of this technology for specific research or commercial applications has yet to be realized. In this review, we discuss the potential applications of nanohole sensor array technology and the impact of that each application has on nanohole array sensor, instrument and assay design. A specific example presented is a multiplexed biomarker assay for metastatic melanoma, which focuses on biomarker specificity in human serum and ultimate levels of detection. This example demonstrates strategies for chip layout and the integration of microfluidic channels to take advantage of the high spatial resolution achievable with this technique. Finally, we evaluate the potential of nanohole array sensor technology against current trends in SPR and protein micro-arrays, providing direction towards development of this tool to fill unmet needs in protein analysis. © 2010 Springer-Verlag.

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