1,720,995 research outputs found
Carbon Negative Method To Synthesize Commodity Chemicals From Carbon Dioxide and Sunlight
Get PDFNano-biohybrid organisms (nanorgs) are a novel, clean energy technology that has been pioneered and developed to success here in our lab. Nanorgs merge photocatalysis and biocatalysis to create a technology that is selective in product generation, utilizes a clean, renewable source of energy, and is highly efficient in terms of material conservation. We show that we are able to synthesize a wide range of commodity chemicals including fertilizers, biopolymers, specialty gases, drop-in fuels, and even biodiesel from only using sunlight and small readily available molecular substrates such as CO2 and N2. This technology works by merging designed quantum dots with living bacteria to create a nano-biohybrid. We find that if the quantum dots are designed with the proper functionality, they are able to migrate inside the cells, attach to product-based proteins specifically targeted, and inject photogenerated electrons into their reaction center. This leads to product generation and alleviates the need for any cellular or natural energetic substrates the organism would normally use (ATP, NADH, etc.), essentially transforming the microbe into an artificially photosynthetic one.
Quantum dots were chosen to use as the photocatalyst because of their small size and easily customizable optical, electronic, and physiological properties. Much of the work behind this technology has gone into designing such quantum dots so that they may be amenable to living cell conditions while being able to power the microbes themselves. We began using III-V and II-VI semiconductor-based quantum dots such as CdS, CdSe, and InP as the core materials. These materials were chosen because of their optoelectronic properties which met specific criteria necessary for proper formation and successive product generation of the nano-biohybrid organisms. By using 2 monolayers of ZnS shell, we are able to control the optoelectronic properties to reach sufficient charge-injection of photogenerated electrons into targeted proteins. The ZnS also serves as a barrier to shield the bacteria from potentially toxic core-materials such as Cd or In in high enough concentrations. Cysteine was chosen as the capping ligand to not only provide colloidal stability for the quantum dots, but also provide them with biocompatibility when interacting with intracellular machinery. Three different ligands were screened, each with varying charges. 3-mercaptopropionic acid (MPA) possesses a negative charge, cysteamine possesses a positive charge, and cysteine is a zwitterion having both negative and positive. Both MPA and cysteamine proved to be quite toxic even at minute concentrations of quantum dots. We owed this to their lack of amenability to varying intracellular conditions, likely causing them to as as sticky pads for positively or negatively charge species within the cell, inducing disruptions in their natural function. This was not the case in the zwitterion cysteine, which showed acceptable levels of biocompatibility at moderate concentrations of quantum dots, causing only minor concerns with the overall health of the cultures. Thus, our optimized quantum dots consisted of a II-VI or III-V semiconductor core material, two monolayers of ZnS, and cysteine capping ligand. These materials proved to work quite well in A. vinelandii and C. necator, pushing quantum efficiencies of up to 13%, rivaling that of some of the best solar cells on the market.
Once we had proven that the concept of nano-biohybrid organisms was successful, we began to review our current process and seek ways in which we could bring this technology closer to commercial applications. One bottle neck for this leap of success is our reliance on relatively expensive materials for the photosensitizer portion of the nanorgs. We began to explore alternative materials that would provide the same level of efficiency but would essentially cost less to develop. Initially we tried gold nanoclusters as their properties were quite similar to that of the quantum dots we were currently using, only their synthesis process was much more eco-friendly. These proved to be successful, and not only did we eliminate our need to rely on expensive designer quantum dots, but the efficiencies seen with Au NCs actually surpassed that of the QDs reaching up to 30% quantum efficiency. This was a huge leap forward, but we were still concerned by the simple cost of the material itself since Au is one of the most expensive metals to date.
We finally landed on carbon quantum dots as our “holy grail” material. They are coveted for this application because they are extremely cheap and easy to make, efficient in their optoelectronic properties, and are largely benign to living organisms since they are mostly made up of carbon. Previously, we had relied on metal – protein residue interactions to provide specific enzymatic targeting of the nanomaterials which was quite successful. In the case of carbon quantum dots this was quite a challenge because naturally there is no metal ion surface and their functional groups closely resemble that of a protein residue. Encasing the carbon quantum dots in the ZnS shell as done previously would not work because of the drastic lattice mismatch between the two species. Scouring the literature, we came across papers that utilized carbon quantum dots as detectors for metal ions in aqueous solutions. Once metal ions attach to functional groups across the surface of the CQDs, their fluorescent signature is quenched, resulting in a quantitative means of detection. Because of this mechanism, we hypothesized that this metal ion surface attachment could provide us with similar coupling-properties seen in previous metal-based QDs which coordinated through their Au- or Zn-rich surfaces. Indeed, we found that CQDs with Ni2+ ions on their surface permitted proper nanorg formation and were able to churn out products on a similar level seen with Au NCs. Without metal ions on their surface enzyme-quantum dot coupling was simply not possible due to limited interactions and lack of affinity between the two. This marked a huge improvement for nanorgs in terms of commercial feasibility. We can now synthesize our sensitizers from very simple an inexpensive starting material such as citric acid or thiourea in contrast to harmful and expensive ones such as CdO.
The starting materials for making CQDs are vast, ranging from citric acid to thiourea to spinach leaves to orange juice. What is even more notable is the fact that they can even be synthesized from proteins through hydrothermal treatment. This idea sparked an additional thrust to increase commercial viability in nanorgs. If we could use excess cell debris once a nanorg production reaction is finished to re-create CQDs and essentially regenerate our system for further production, this would surely increase the commercial viability as well. Not only that, but it would result in a carbon-negative process that would continually excavate CO2 and not only put it into usable products but be used to re-grow the bacteria and ultimately re-synthesize CQDs to completely regenerate our system.
Taking cell debris of C. necator after a large-scale PHB generating reaction, we lysed the cells and removed any large debris that might hinder the formation of CQDs. After isolating a broad range of proteins through centrifugal filtering, we subject the remaining debris to hydrothermal treatment for a few hours and filtered out any large particles by centrifugation, leaving a supernatant filled with CQDs. Measuring the optical properties, these CQDs seem quite similar to CQDs synthesized traditionally through thermolysis of citric acid and thiourea. We then put them to the test in ethylene-generating nanorgs, complexing them with Ni2+ prior to nanorg formation. We found that their production was right on par with CQDs formed in the more traditional method. These results coupled with ones previously seen in the impressive performance of CQD nanorgs marks a huge leap forward in the commercial viability of nanorgs as a whole.</p
Carbon Negative Method To Synthesize Commodity Chemicals From Carbon Dioxide and Sunlight
Get PDFNano-biohybrid organisms (nanorgs) are a novel, clean energy technology that has been pioneered and developed to success here in our lab. Nanorgs merge photocatalysis and biocatalysis to create a technology that is selective in product generation, utilizes a clean, renewable source of energy, and is highly efficient in terms of material conservation. We show that we are able to synthesize a wide range of commodity chemicals including fertilizers, biopolymers, specialty gases, drop-in fuels, and even biodiesel from only using sunlight and small readily available molecular substrates such as CO2 and N2. This technology works by merging designed quantum dots with living bacteria to create a nano-biohybrid. We find that if the quantum dots are designed with the proper functionality, they are able to migrate inside the cells, attach to product-based proteins specifically targeted, and inject photogenerated electrons into their reaction center. This leads to product generation and alleviates the need for any cellular or natural energetic substrates the organism would normally use (ATP, NADH, etc.), essentially transforming the microbe into an artificially photosynthetic one.
Quantum dots were chosen to use as the photocatalyst because of their small size and easily customizable optical, electronic, and physiological properties. Much of the work behind this technology has gone into designing such quantum dots so that they may be amenable to living cell conditions while being able to power the microbes themselves. We began using III-V and II-VI semiconductor-based quantum dots such as CdS, CdSe, and InP as the core materials. These materials were chosen because of their optoelectronic properties which met specific criteria necessary for proper formation and successive product generation of the nano-biohybrid organisms. By using 2 monolayers of ZnS shell, we are able to control the optoelectronic properties to reach sufficient charge-injection of photogenerated electrons into targeted proteins. The ZnS also serves as a barrier to shield the bacteria from potentially toxic core-materials such as Cd or In in high enough concentrations. Cysteine was chosen as the capping ligand to not only provide colloidal stability for the quantum dots, but also provide them with biocompatibility when interacting with intracellular machinery. Three different ligands were screened, each with varying charges. 3-mercaptopropionic acid (MPA) possesses a negative charge, cysteamine possesses a positive charge, and cysteine is a zwitterion having both negative and positive. Both MPA and cysteamine proved to be quite toxic even at minute concentrations of quantum dots. We owed this to their lack of amenability to varying intracellular conditions, likely causing them to as as sticky pads for positively or negatively charge species within the cell, inducing disruptions in their natural function. This was not the case in the zwitterion cysteine, which showed acceptable levels of biocompatibility at moderate concentrations of quantum dots, causing only minor concerns with the overall health of the cultures. Thus, our optimized quantum dots consisted of a II-VI or III-V semiconductor core material, two monolayers of ZnS, and cysteine capping ligand. These materials proved to work quite well in A. vinelandii and C. necator, pushing quantum efficiencies of up to 13%, rivaling that of some of the best solar cells on the market.
Once we had proven that the concept of nano-biohybrid organisms was successful, we began to review our current process and seek ways in which we could bring this technology closer to commercial applications. One bottle neck for this leap of success is our reliance on relatively expensive materials for the photosensitizer portion of the nanorgs. We began to explore alternative materials that would provide the same level of efficiency but would essentially cost less to develop. Initially we tried gold nanoclusters as their properties were quite similar to that of the quantum dots we were currently using, only their synthesis process was much more eco-friendly. These proved to be successful, and not only did we eliminate our need to rely on expensive designer quantum dots, but the efficiencies seen with Au NCs actually surpassed that of the QDs reaching up to 30% quantum efficiency. This was a huge leap forward, but we were still concerned by the simple cost of the material itself since Au is one of the most expensive metals to date.
We finally landed on carbon quantum dots as our “holy grail” material. They are coveted for this application because they are extremely cheap and easy to make, efficient in their optoelectronic properties, and are largely benign to living organisms since they are mostly made up of carbon. Previously, we had relied on metal – protein residue interactions to provide specific enzymatic targeting of the nanomaterials which was quite successful. In the case of carbon quantum dots this was quite a challenge because naturally there is no metal ion surface and their functional groups closely resemble that of a protein residue. Encasing the carbon quantum dots in the ZnS shell as done previously would not work because of the drastic lattice mismatch between the two species. Scouring the literature, we came across papers that utilized carbon quantum dots as detectors for metal ions in aqueous solutions. Once metal ions attach to functional groups across the surface of the CQDs, their fluorescent signature is quenched, resulting in a quantitative means of detection. Because of this mechanism, we hypothesized that this metal ion surface attachment could provide us with similar coupling-properties seen in previous metal-based QDs which coordinated through their Au- or Zn-rich surfaces. Indeed, we found that CQDs with Ni2+ ions on their surface permitted proper nanorg formation and were able to churn out products on a similar level seen with Au NCs. Without metal ions on their surface enzyme-quantum dot coupling was simply not possible due to limited interactions and lack of affinity between the two. This marked a huge improvement for nanorgs in terms of commercial feasibility. We can now synthesize our sensitizers from very simple an inexpensive starting material such as citric acid or thiourea in contrast to harmful and expensive ones such as CdO.
The starting materials for making CQDs are vast, ranging from citric acid to thiourea to spinach leaves to orange juice. What is even more notable is the fact that they can even be synthesized from proteins through hydrothermal treatment. This idea sparked an additional thrust to increase commercial viability in nanorgs. If we could use excess cell debris once a nanorg production reaction is finished to re-create CQDs and essentially regenerate our system for further production, this would surely increase the commercial viability as well. Not only that, but it would result in a carbon-negative process that would continually excavate CO2 and not only put it into usable products but be used to re-grow the bacteria and ultimately re-synthesize CQDs to completely regenerate our system.
Taking cell debris of C. necator after a large-scale PHB generating reaction, we lysed the cells and removed any large debris that might hinder the formation of CQDs. After isolating a broad range of proteins through centrifugal filtering, we subject the remaining debris to hydrothermal treatment for a few hours and filtered out any large particles by centrifugation, leaving a supernatant filled with CQDs. Measuring the optical properties, these CQDs seem quite similar to CQDs synthesized traditionally through thermolysis of citric acid and thiourea. We then put them to the test in ethylene-generating nanorgs, complexing them with Ni2+ prior to nanorg formation. We found that their production was right on par with CQDs formed in the more traditional method. These results coupled with ones previously seen in the impressive performance of CQD nanorgs marks a huge leap forward in the commercial viability of nanorgs as a whole.</p
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Design of a De Novo Aggregating Antimicrobial Peptide and a Bacterial Conjugation-Based Delivery System
Get PDFAntibacterial resistance necessitates the development of novel treatment methods for infections. Protein aggregates have recently been applied as antimicrobials to disrupt bacterial homeostasis. Past work on protein aggregates has focused on genome mining for aggregation-prone sequences in bacterial genomes rather than on rational design of aggregating antimicrobial peptides. Here, we use a synthetic biology approach to design an artificial gene encoding a de novo aggregating antimicrobial peptide. This artificial gene, opaL (overexpressed protein aggregator Lipophilic), disrupts bacterial homeostasis by expressing extremely hydrophobic peptides. When this hydrophobic sequence is disrupted by acidic residues, consequent aggregation and antimicrobial effect decreases. Further, we developed a probiotic delivery system using the broad-host range conjugative plasmid RK2 to transfer the gene from donor to recipient bacteria. We utilize RK2 to mobilize a shuttle plasmid carrying opaL by adding the RK2 origin of transfer. We show that opaL is non-toxic to the donor, allowing for maintenance and transfer since its expression is under control of a promoter with a recipient-specific T7 RNA polymerase. Upon mating of donor and recipient Escherichia coli, we observe selective growth repression in T7 polymerase-expressing recipients. This technique could be used to target desired pathogens by selecting pathogen-specific promoters to control T7 RNA polymerase expression and provides a basis for the design and delivery of aggregating antimicrobial peptides
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Design of a De Novo Aggregating Antimicrobial Peptide and a Bacterial Conjugation-Based Delivery System
Get PDFAntibacterial resistance necessitates the development of novel treatment methods for infections. Protein aggregates have recently been applied as antimicrobials to disrupt bacterial homeostasis. Past work on protein aggregates has focused on genome mining for aggregation-prone sequences in bacterial genomes rather than on rational design of aggregating antimicrobial peptides. Here, we use a synthetic biology approach to design an artificial gene encoding a de novo aggregating antimicrobial peptide. This artificial gene, opaL (overexpressed protein aggregator Lipophilic), disrupts bacterial homeostasis by expressing extremely hydrophobic peptides. When this hydrophobic sequence is disrupted by acidic residues, consequent aggregation and antimicrobial effect decreases. Further, we developed a probiotic delivery system using the broad-host range conjugative plasmid RK2 to transfer the gene from donor to recipient bacteria. We utilize RK2 to mobilize a shuttle plasmid carrying opaL by adding the RK2 origin of transfer. We show that opaL is non-toxic to the donor, allowing for maintenance and transfer since its expression is under control of a promoter with a recipient-specific T7 RNA polymerase. Upon mating of donor and recipient Escherichia coli, we observe selective growth repression in T7 polymerase-expressing recipients. This technique could be used to target desired pathogens by selecting pathogen-specific promoters to control T7 RNA polymerase expression and provides a basis for the design and delivery of aggregating antimicrobial peptides
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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