Molecular Sequestration Research Articles

Selective Uptake and Refolding of Globular Proteins in Coacervate Microdroplets

Intrinsic differences in the molecular sequestration of folded and unfolded proteins within poly(diallyldimethylammonium) (PDDA)/poly(acrylate) (PAA) coacervate microdroplets are exploited to establish membrane-free microcompartments that support protein refolding, facilitate the recovery of secondary structure and enzyme activity, and enable the selective uptake and exclusion of folded and unfolded biomolecules, respectively. Native bovine serum albumin, carbonic anhydrase, and α-chymotrypsin are preferentially sequestered within positively charged coacervate microdroplets, and the unfolding of these proteins in the presence of increasing amounts of urea results in an exponential decrease in the equilibrium partition constants as well as the kinetic release of unfolded molecules from the droplets into the surrounding continuous phase. Slow refolding in the presence of positively charged microdroplets leads to the resequestration of functional proteins and the restoration of enzymatic activity; however, fast refolding results in protein aggregation at the droplet surface. In contrast, slow and fast refolding in the presence of negatively charged PDDA/PAA droplets gives rise to reduced protein aggregation and misfolding by interactions at the droplet surface to give increased levels of protein renaturation. Together, our observations provide new insights into the bottom-up design and construction of self-assembling microcompartments capable of supporting the selective uptake and refolding of globular proteins.

Designed Functional Lipidic Biomaterials: Applications in Molecular Recognition, Drug Delivery and Membrane Protein Crystallization

A large library of lipids with novel functionalities was designed and synthesized in order to investigate the effects of lipid structure on the ensuing nanomaterial structure, dynamics, stability and phase behavior. These were assembled within lipidic mesophases and their dispersions, forming biomaterials that were effectively used in areas ranging from molecular recognition, sequestration and enrichment of nucleic acids to biosensing and fuel cells. An exciting new class of biomaterials that are based on cyclopropanated lipids was developed. These form stable lipidic cubic phases (LCPs) at low temperature, opening the way to conduct biophysical and biochemical investigations on temperature sensitive bio-macromolecules. Furthermore, pH-sensitive lipidic matrices for hydrophilic as well as hydrophobic drug incorporation and release were designed, as well as stimuli-responsive lipids that can be incorporated into biomaterials, rendering them stimuli-responsive. Efficient pH- and light-induced binding, release and sequestration of hydrophilic dyes were demonstrated. Significantly, these processes could be activated sequentially, thereby achieving both temporal and dosage control. Finally, a new light responsive, host-guest delivery system was developed, in which single step as well as sequential light-triggered release and retention of an embedded hydrophilic dye upon irradiation with UV and visible light can be affected.

Nonspecific transcription factor binding can reduce noise in the expression of downstream proteins

Transcription factors (TFs) interact with a multitude of binding sites on DNA and partner proteins inside cells. We investigate how nonspecific binding/unbinding to such decoy binding sites affects the magnitude and time-scale of random fluctuations in TF copy numbers arising from stochastic gene expression. A stochastic model of TF gene expression, together with decoy site interactions is formulated. Distributions for the total (bound and unbound) and free (unbound) TF levels are derived by analytically solving the chemical master equation under physiologically relevant assumptions. Our results show that increasing the number of decoy binding sides considerably reduces stochasticity in free TF copy numbers. The TF autocorrelation function reveals that decoy sites can either enhance or shorten the time-scale of TF fluctuations depending on model parameters. To understand how noise in TF abundances propagates downstream, a TF target gene is included in the model. Intriguingly, we find that noise in the expression of the target gene decreases with increasing decoy sites for linear TF-target protein dose-responses, even in regimes where decoy sites enhance TF autocorrelation times. Moreover, counterintuitive noise transmissions arise for nonlinear dose-responses. In summary, our study highlights the critical role of molecular sequestration by decoy binding sites in regulating the stochastic dynamics of TFs and target proteins at the single-cell level.

Cognitive impairments in common and rare somatic diseases

The paper gives an update on the pathogenesis, clinical presentation, and pathomorphology of cognitive impairments (CIs) in different autoimmune, endocrine, and infectious diseases, such as systemic lupus erythematosus, Sjögren's syndrome, BehНet's disease, primary angiitis of the central nervous system, polyarteritis nodosa, cryoglobulinemic vasculitis, hypothyroidism, herpetic lesion, and neurosyphilis. These patients are observed to have ischemic-hypoxic brain damage, the causes of which are free radical-induced cell injury, oxidative stress, excitation toxicity, cell necrosis and/or apoptosis, inflammation and immune disease, molecular sequestration, and cell death. There is enhanced imbalance in the pro-oxidant and antioxidant systems as cerebrovascular insufficiency progresses; as this takes place, the nerve cells are most susceptible to the induction of free radical reactions. In these cases, antioxidants that block the effects of free radicals and may potentially improve brain perfusion, by assisting the coupling of neurons and vessels, are first-choice drugs. To improve the cognitive status and to prevent the progression of CIs, it is important to build a cognitive reserve in a patient; this is largely favored by the preservation of a proactive approach to life and social bonds, as well as intellectual work.

Spatial Organization and Mechanical Properties of the Pericellular Matrix on Chondrocytes

A voluminous polymer coat adorns the surface of many eukaryotic cells. Although the pericellular matrix (PCM) often extends several microns from the cell surface, its macromolecular structure remains elusive. This massive cellular organelle negotiates the cell’s interaction with surrounding tissue, influencing important processes such as cell adhesion, mitosis, locomotion, molecular sequestration, and mechanotransduction. Investigations of the PCM’s architecture and function have been hampered by the difficulty of visualizing this invisible hydrated structure without disrupting its integrity. In this work, we establish several assays to noninvasively measure the ultrastructure of the PCM. Optical force probe assays show that the PCM of rat chondrocyte joint (RCJ-P) cells easily reconfigures around optically manipulated microparticles, allowing the probes to penetrate into rather than compress the matrix. We report distinct changes in forces measured from PCMs treated with exogenous aggrecan, illustrating the assay’s potential to probe proteoglycan distribution. Measurements reveal an exponentially increasing osmotic force in the PCM arising from an inherent concentration gradient. With this result, we estimate the variation of the PCM’s mesh size (correlation length) to range from ∼100 nm at the surface to 500 nm at its periphery. Quantitative particle exclusion assays confirm this prediction and show that the PCM acts like a sieve. These assays provide a much-needed tool to study PCM ultrastructure and its poorly defined but important role in fundamental cellular processes.

Synergistic dual positive feedback loops established by molecular sequestration generate robust bimodal response

Feedback loops are ubiquitous features of biological networks and can produce significant phenotypic heterogeneity, including a bimodal distribution of gene expression across an isogenic cell population. In this work, a combination of experiments and computational modeling was used to explore the roles of multiple feedback loops in the bimodal, switch-like response of the Saccharomyces cerevisiae galactose regulatory network. Here, we show that bistability underlies the observed bimodality, as opposed to stochastic effects, and that two unique positive feedback loops established by Gal1p and Gal3p, which both regulate network activity by molecular sequestration of Gal80p, induce this bimodality. Indeed, systematically scanning through different single and multiple feedback loop knockouts, we demonstrate that there is always a concentration regime that preserves the system's bimodality, except for the double deletion of GAL1 and the GAL3 feedback loop, which exhibits a graded response for all conditions tested. The constitutive production rates of Gal1p and Gal3p operate as bifurcation parameters because variations in these rates can also abolish the system's bimodal response. Our model indicates that this second loss of bistability ensues from the inactivation of the remaining feedback loop by the overexpressed regulatory component. More broadly, we show that the sequestration binding affinity is a critical parameter that can tune the range of conditions for bistability in a circuit with positive feedback established by molecular sequestration. In this system, two positive feedback loops can significantly enhance the region of bistability and the dynamic response time.

A Roadmap for Addressing Environmental and Social Issues Associated With Horizontal Drilling and Hydraulic Fracturing

R&D Grand Challenges - This is the latest in a series of articles on the great challenges facing the oil and gas industry as outlined by the SPE Research and Development (R&D) Committee. The R&D challenges comprise broad upstream business needs: increasing recovery factors, in-situ molecular manipulation, carbon capture and sequestration, produced water management, higher resolution subsurface imaging of hydrocarbons, and the environment. The articles in this series examine each of these challenges in depth. The R&D Grand Challenges Series, comprising articles published in JPT during 2011 and 2012, is available as a collection on OnePetro (SPE-163061-JPT). The energy industry faces a massive communications challenge in persuading sizeable sections of the public in the United States and overseas that natural gas operations relying on horizontal drilling and hydraulic fracturing can be conducted safely. Mitchell Energy founder George Mitchell has stated that industry has “the duty to fracture responsibly.” He was candid when he said, “There is no question that accidents have occurred and mistakes have been made during the rush to develop.” Mitchell’s candor was remarkable because, for too many years, the industry has mainly responded to attacks on shale gas operations by pointing out errors or omissions in critical media accounts. The industry has also emphasized the 60-year history of hydraulic fracturing while ignoring the growth of legitimate public concerns arising from the exponential growth of combined horizontal drilling and hydraulic fracturing during the past 15 years. Thoughtful companies recognize that this has not been a successful strategy for building public trust, and they are beginning to speak directly to the real risks associated with their operations. These real risks include, for example, poor cementing practices in well construction and inadequate waste-water management. Since mid-2009, investors have been seeking increased disclosure by companies of the environmental and social risks associated with natural gas operations in shale formations and the policies and procedures they are adopting to reduce or eliminate these risks. Risks are associated with the broad life cycle of shale gas operations, not just with hydraulic fracturing as technically defined. Fracturing and horizontal drilling together make substantial recovery of gas from shales economically possible and have brought drilling and production to localities on a scale previously not experienced.

Peptide and RNA contributions to iron–sulphur chemical gardens as life's first inorganic compartments, catalysts, capacitors and condensers

Hydrothermal chimneys and compartments comprising transition metal sulphides and associated minerals have been proposed as likely locations for the beginnings of life. In laboratory simulations of off-axis alkaline springs, it is shown that the interaction of a simulated alkaline sulphide-bearing submarine vent solution with a primeval anoxic iron-bearing ocean leads to the formation of chimney structures reminiscent of chemical gardens. These chimneys display periodicity in their deposition and exhibit diverse morphologies and mineralogies, affording the possibilities of catalysis and molecular sequestration. The addition of peptides and RNA to the alkaline solution modifies the elemental stoichiometry of the chimneys-perhaps indicating the very initial stage of the organic takeover on the way to living cells by charged organic polymers potentially synthesized in this same environment.

Grand Challenges for Earth Resources Engineering

R&D Grand Challenges - During 2010, the SPE Research and Development (R&D) Committee developed a list of some of the great challenges facing the oil and gas industry. The committee prioritized these needs and called them the ’R&D Grand Challenges’: increasing recovery factors, in-situ molecular manipulation, carbon capture and sequestration, produced water management, higher resolution subsurface imaging of hydrocarbons, and the environment. These ’grand challenges’ incorporate as much as possible enabling technologies (e.g., drilling performance can improve recovery) as well as address the technical disciplines within the SPE organization - Drilling and Completions; Facilities and Construction; Reservoir Description and Dynamics; Production and Operations; Health, Safety, and the Environment; and Management and Information. It is the intent of the SPE R&D Committee to articulate and promote the benefits of R&D in the upstream oil and gas industry so this third series of invited guest JPT articles was begun in May 2011. These have been published every two or three months with two remaining articles to appear. The R&D Grand Challenges Series, comprising articles published in JPT during 2011 and 2012, is available as a collection on OnePetro (SPE-163061-JPT). A recent report by the US National Academy of Engineering (Grand Challenges for Engineering, NAE 2008) identified 14 grand challenges covering the broad range of engineering disciplines that await engineering solutions and that, when accomplished, will make significant improvements to the broad realms of human concern: sustainability, health, vulnerability, and joy of living. Two of those challenges are in Earth resources engineering: developing carbon sequestration methods and providing clean water. Many other engineering challenges fall into the category of Earth resources engineering so a task force composed of members of the academy’s Earth Resources Section identified four challenges that were the most critical. They are: Make the Earth transparent. Understand, engineer, and control subsurface coupled processes. Minimize the environmental footprint. Protect people. The primary objective of Earth resources engineering is to apply engineering principles to the discovery, development, and environmentally responsible production of subsurface Earth resources. The traditional engineering disciplines for this objective are mining engineering, mineral processing engineering, petroleum engineering, and geological engineering. However, other science and engineering disciplines contribute critical expertise, particularly geophysics and hydrogeology. The skills needed to explore and produce resources from the Earth are also important in the study of earthquakes, the subsurface flow of groundwater, the storage of wastes such as carbon dioxide or nuclear wastes, and the design of subsurface structures for human habitat or subsurface infrastructure such as electrical cables or pipelines. Make the Earth Transparent That the solid Earth is opaque is a major obstacle in all aspects of Earth resources engineering. The challenge for subsurface engineering is similar to the imaging problem in medicine. We need tools that will allow us to see into the subsurface just as medical tools allow doctors to see into the human body. Geological structures range from the microscopic grains and crystals of the rock matrix and associated pore spaces to the topography of a basin. This range spans nanometers to kilometers, or 12 factors of 10. To complicate matters further, geological properties are mostly anisotropic (vary with direction) and heterogeneous (vary in space). Because of the scale effect, many methods and tools are required to characterize geological structures. On the largest scale (1–10 km spatial resolution), airborne gravity, magnetic and electromagnetic imaging, and satellite-based synthetic aperture radar measurements are used. On the scale of 10–100 m, seismic waves are used, either actively generated by explosive charges or mechanical vibrators or naturally generated by distant earthquakes or ocean waves. On a smaller scale of centimeters to 1 m, a variety of well logging tools that use electromagnetic, nuclear, and gamma ray technology exist.

Unconventional Resources: Cracking the Hydrocarbon Molecules In Situ

R&D Grand Challenges - This is the sixth in a series of articles on the great challenges facing the oil and gas industry as outlined by the SPE Research and Development (R&D) Committee.The R&D challenges comprise broad upstream business needs: increasing recovery factors, in-situ molecular manipulation, carbon capture and sequestration, produced water management, higher resolution subsurface imaging of hydrocarbons, and the environment. The articles in this series examine each of these challenges in depth. The R&D Grand Challenges Series, comprising articles published in JPT during 2011 and 2012, is available as a collection on OnePetro (SPE-163061-JPT). Discoveries of accumulations of light crude oil are dwindling, and known resources are increasingly concentrated in areas that are predominantly accessible by state-owned or state-affiliated energy companies. As a result, the quality of (conventional) crude oil—particularly oil sourced from non-OPEC reservoirs—has been declining. The trend is bound to accelerate as unconventional hydrocarbons such as bitumen are brought into production to satisfy the world’s energy demand, which is expected to increase by slightly less than 50% in the next 20 years. Because the recovery and surface processing of these heavier molecules is more difficult, it is appropriate to ask whether a portion of the surface processing can be performed downhole (in situ). In fact, in the case of deeper-lying oil shale, it is the only realistic recovery option. There are three approaches by which in-situ manipulation of molecules can be accomplished: biological, chemical, and thermal. Although this article focuses on the thermal route, it should be noted that hybrid recovery methods may be more effective in satisfying the requirement to maximize economic value while minimizing water consumption, emissions, and land usage. The oil sands of Alberta, Canada, and the oil shale deposits in Colorado contain volumes of hydrocarbons that are at least comparable to the conventional oil resources in the Middle East (Fig. 1). Extraction by open pit mining is the dominant recovery method for commercial exploitation of the oil sands and is the only commercially practiced recovery method for oil shale. However, 70% to 80% of the oil sands in Alberta are deposited at intervals that are too deep (deeper than 60 m) to mine economically, and the same holds true for the richest and thickest sections of oil shale (deeper than 1,000 ft). Ever-increasing concerns about the environmental impact of mining (soil removal, tailings ponds, etc.) provide additional incentives toward the use of in-situ recovery methods.

Higher Resolution Subsurface Imaging

R&D Grand Challenges - This is the fifth in a series of articles on the great challenges facing the oil and gas industry as outlined by the SPE Research and Development (R&D) Committee. The R&D challenges comprise broad upstream business needs: increasing recovery factors, in-situ molecular manipulation, carbon capture and sequestration, produced water management, higher resolution subsurface imaging of hydrocarbons, and the environment. The articles in this series examine each of these challenges in depth. The R&D Grand Challenges Series, comprising articles published in JPT during 2011 and 2012, is available as a collection on OnePetro (SPE-163061-JPT). Introduction It is hard to read road signs if you have poor eyesight, which is why driver’s licenses are issued with restrictions requiring that corrective lenses must be worn. Likewise, it is hard to find and exploit subsurface resources if you can’t clearly see your targets or monitor the movement of fluids in the reservoir. Engineers now have powerful tools to precisely model subsurface reservoir production behavior, but a precise answer is still wrong if it is derived from an inaccurate subsurface description. Geoscientists make maps and rock property models of the subsurface by interpreting images that are produced from remote sensing data. Analogs from modern depositional environments and outcrop exposures guide subsurface data interpretation to predict ahead of the bit, then postdrill geostatistics are used to fill in stratigraphic details between wellbore control points. Selection of the right depositional model, facies distribution, and geostatistical analog depends on having the sharpest, most detailed and accurate image of the subsurface possible—the Grand Challenge of Higher Resolution Subsurface Imaging. Over the past century, the industry has relentlessly sought ways to improve subsurface imaging of hydrocarbons. Canadian inventor Reginald Fessenden first patented the use of the seismic method to infer geology in 1917. A decade later, Schlumberger lowered an electric tool down a borehole in France to record the first well log. Today, advances in seismic and gravity data acquisition, electromagnetics, signal processing and modeling powered by high-performance computing, and the nanotechnology revolution are at the forefront of improved reservoir imaging. In this paper, we will examine the challenges of getting higher resolution subsurface images of hydrocarbons and touch on emerging research trends and technologies aimed at delivering a more accurate reservoir picture.

Can Geoscientists Resolve the CCS Paradox?

R&D Grand Challenges - This is the fourth in a series of articles on the great challenges facing the oil and gas industry as outlined by the SPE Research and Development (R&D) Committee. The R&D challenges comprise broad upstream business needs: increasing recovery factors, in-situ molecular manipulation, carbon capture and sequestration, produced water management, higher resolution subsurface imaging of hydrocarbons, and the environment. The articles in this series examine each of these challenges in depth. The R&D Grand Challenges Series, comprising articles published in JPT during 2011 and 2012, is available as a collection on OnePetro (SPE-163061-JPT). International energy and climate organizations have found carbon capture and storage (CCS) to be a promising technology to resolve the squeeze between fast-growing global energy needs and global warming. Even environmental organizations say that making our energy use more efficient and building enough new renewable energy capacity takes too long. We need to get the CCS working to curb the growing greenhouse gas emissions if too large a climate change is to be avoided. CCS consists of three major interdependent steps: Capture the carbon, CO2 out of flue gases, either from the stack of a power plant or the blast furnace top gas in iron making. Transport it by pipeline or ship it underground. Safely keep it in a storage site for thousands of years. The technology for each of these steps has been used for decades in the industry, mostly in oil and gas. The important change is the scale—from about 100,000 to 1 million metric tons per year in the past. Today, we see the need for handling 10 million tons in each installation and for perhaps several thousand installations. The amount of CO2 produced from one power station varies from 2 million to 10 million tons; a modern iron-making blast furnace emits up to 10 million tons per year. The costs of the technologies for a large-scale CO2 handling chain are estimated to be split roughly 75%-10%-15% for capture-transport-storage.

Selective Molecular Sequestration with Concurrent Natural Product Functionalization and Derivatization: From Crude Natural Product Extracts to a Single Natural Product Derivative in One Step

A resin-bound nitroso compound sequestered a single unexpected component from crude plant seed extracts. Several plants, including Piper nigrum, Eugenia caryophyllata, and Pimenta dioica, were extracted with organic solvent in the presence of a nitroso-containing resin. The nitroso resin selectively sequestered a single compound, β-caryophyllene, via a chemo- and regioselective ene reaction. The ene product was released from the resin, and proper selection of the solid-phase linker and cleavage cocktail allowed concomitant further transformation of the primary ene product to a novel functionalized polycycle. Preliminary studies indicate that the new hydroxylamine-containing natural product derivatives have antibiotic activity.

Brine Management: Produced Water and Frac Flowback Brine

R&D Grand Challenges - This is the third in a series of articles on the great challenges facing the oil and gas industry as outlined by the SPE Research and Development (R&D) Committee. The R&D challenges comprise broad upstream business needs: increasing recovery factors, in-situ molecular manipulation, carbon capture and sequestration, produced water management, higher resolution subsurface imaging of hydrocarbons, and the environment. The articles in this series examine each of these challenges in depth. The R&D Grand Challenges Series, comprising articles published in JPT during 2011 and 2012, is available as a collection on OnePetro (SPE-163061-JPT). White papers covering these challenges are available at www.spe.org/industry/globalchallenges and allow reader comments and open discussion of the topics. White papers are currently available on the subjects of in-situ molecular manipulation, increasing hydrocarbon recovery factors, and carbon capture and sequestration with additional papers to be added in coming months. The world is changing. The transformation from onshore infill drilling and occasional field extension operations to the rapid development of super major gas fields throughout the United States is being called the great gas shale revolution. This disruptive change is as significant as the advent of rotary drilling in the 19th century. Three issues drive this revolution: The world’s energy needs are increasing at an exponential rate and, led by the US and the European Union, there is a major thrust to move toward clean energy. In the US, vast reserves of unconventional gas are technically recover-able within its own boundaries and that energy security is one of its benefits. Most important, technology to access these resources is advancing at an increasing rate. Today we are seeing major developments—not only the Barnett Shale, but also the Fayetteville, Haynesville, Eagle Ford, and Marcellus shales in North America. Together, these and other developing and prospective gas shale plays offer the US more than a 400-year supply of this abundant, clean-burning fuel. So why is there a controversy over development of these resources? One issue stands out—the environmental footprint of unconventional gas development. Along with this new awareness of the availability of abundant energy, the environmental impact of energy production is a critical part of the equation.

Relative Efficacy of High-Pressure Hot Water and High-Power Ultrasonics for Wine Oak Barrel Sanitization

<h3>Abstract</h3> Engineered genetic circuits with tailored functions that mimic how cells process information in changing environments (e.g. cell fate decision, chemotaxis, immune response) have great applications in biomedicine and synthetic biology. Although there is a lot of progress toward the design of gene circuits yielding desired steady states (e.g. logic-based networks), building synthetic circuits for dynamic signal processing (e.g. filters, frequency modulation, and controllers) is still challenging. Here, we provide a model-based approach to build gene networks that can operate as band-pass filters by taking advantage of molecular sequestration. By suitably approximating the dynamics of molecular sequestration, we analyze an Incoherent Feed-Forward Loop (IFFL) and a Negative Feedback (NF) circuit and illustrate how they can achieve band-pass filter behavior. Computational analysis shows that a circuit that incorporates both IFFL and NF motifs improves the filter performance. Our approach facilitates the design of sequestration-based filters, and may support the synthesis of molecular controllers with desired specifications.

Recent Developments and Remaining Challenges of Enhanced Oil Recovery

R&amp;D Grand Challenges - This is the second in a series of articles on the great challenges facing the oil and gas industry as outlined by the SPE R&amp;D Committee. The R&amp;D challenges comprise broad upstream business needs: increasing recovery factors, in-situ molecular manipulation, carbon capture and sequestration, produced water management, higher resolution subsurface imaging of hydrocarbons, and the environment. The articles in this series are examining each of these challenges in depth. The R&amp;D Grand Challenges Series, comprising articles published in JPT during 2011 and 2012, is available as a collection on OnePetro (SPE-163061-JPT). The world is changing. Some look back and some look forward. Some look at the challenges of ramping up enhanced oil recovery (EOR) in the past and some look at the opportunities for doing so now. This article will provide a broad view of recent developments and the remaining challenges for readers who are not EOR specialists. There has been a renaissance in chemical EOR during the past few years because of major advances in the technology and high oil prices. Thermal and miscible gas methods are much more mature with the exception of processes such as co-injection of gases and surfactants for mobility control. The synergy between the EOR processes and improved reservoir characterization and formation evaluation, reservoir modeling and simulation, reservoir management, well technology, production methods, and facilities is significant and not as widely recognized as it should be. Polymer flooding is the simplest and most widely used chemical EOR process. Polymer flooding has been used commercially since the 1960s; more oil is produced by polymer flooding than all of the other chemical EOR processes combined. Adding polymer to the water increases its viscosity. The benefit of polymer flooding increases as the oil viscosity and/or the reservoir heterogeneity increases. Polyacrylamide copolymers or hydrolyzed polyacrylamide (HPAM) polymers are by far the most widely used polymer for EOR. Much higher molecular weight HPAM is now available than when it was first used in the 1960s and 1970s. The quality of commercial HPAM polymer has also improved dramatically and the price relative to crude oil has decreased. In the early 1970s, oil sold for about USD 3/bbl and HPAM polymer for about USD 1.50/lb. Now oil is about USD 100/bbl and HPAM stays about the same price. About 1 to 2 lbs of polymer are needed to produce an incremental barrel of oil, which means the polymer cost is about USD 1.50/bbl to USD 3/bbl. This helps explain why the number of polymer floods is increasing exponentially and about 1 billion lbs of polymer will be used for EOR this year. Most early polymer floods were done using very small amounts of polymer (i.e., low polymer concentrations and small pore volumes of polymer solution), but now we know polymer floods perform much better at large polymer concentration.

Medium composition effects on solute partitioning in solid–liquid two‐phase bioreactors

AbstractBiphasic systems such as two‐phase partitioning bioreactors (TPPBs) have been used to alleviate biological inhibition by sequestering inhibitory compounds within an immiscible phase. The use of solid polymer beads as this auxiliary phase provides a fully biocompatible alternative to potentially toxic organic solvents. While guidelines exist for the rational selection of the polymer phase, the effect of the aqueous phase composition on molecular sequestration has not been explored in the literature. This work aims to identify aspects of medium composition that influence the partitioning of target molecules into the sequestering phase. Using benzaldehyde as the target molecule and Hytrel G3548L (DuPont) as the polymer phase, pH, temperature, salt and glucose concentrations, as well as ethanol concentrations, were examined for their effects on the partition coefficient. pH and temperature were observed to have no significant effect on benzaldehyde partitioning. Salt and glucose additions increased the partition coefficient by 173% and 30%, respectively, compared with pure reverse osmosis (RO) water, while increasing ethanol concentration was found to decrease the partition coefficient from 44 ( ± 1.6) to 1 ( ± 0.3). Strategic changes to the aqueous phase can be made to improve affinity of the sequestering phase for target molecules. This provides a simple and cost‐effective method to potentially improve TPPB system performance. Copyright © 2010 Society of Chemical Industry

Catanionic surfactant vesicles for electrostatic molecular sequestration and separation

Mixtures of oppositely charged surfactants, commonly called catanionic mixtures, are one of the most interesting and promising areas of colloidal chemistry. In this paper we review our previous work and report new results on electrostatic adsorption of organic solutes and DNA to the exterior surfaces of catanionic, unilamellar vesicles which form spontaneously in mixtures of sodium dodecylbenzenesulfonate (SDBS) and cetyltrimethylammonium tosylate (CTAT). Our group, along with others, has shown that organic ions and polyelectrolytes will bind to the exterior surface of oppositely charged catanionic vesicles through interactions with unpaired ionic surfactants present in the vesicle bilayer. The electrostatic sequestration of organic ions with catanionic vesicles is extremely efficient with excellent long-term stability and can be used to perform separations on mixtures of charged organic solutes. Using regular solution theory extended to vesicle-forming surfactant mixtures, we can understand how the composition of the bilayer changes with surfactant dilution, and we study this effect using fluorescence correlation spectroscopy (FCS). We employ FCS to make sensitive measurements of bilayer adsorption and compare the adsorption of a small molecular probe with that of a single-stranded, dye-labeled DNA molecule. From these FCS studies, adsorption isotherms can be obtained that report on the relative binding strengths of the two systems. The results show that DNA binds much more strongly to the exterior surface of positively charged catanionic vesicles, and can even stabilize vesicles at very low surfactant concentrations near the critical aggregation concentration (cac).

14-3-3 proteins and plant development.

The 14-3-3 proteins are a family of ubiquitous regulatory molecules which have been found in virtually every eukaryotic organism and tissue. Discovered 34 years ago, 14-3-3 proteins have first been studied in mammalian nervous tissues, but in the past decade their indispensable role in various plant regulatory and metabolic pathways has been increasingly established. We now know that 14-3-3 members regulate fundamental processes of nitrogen assimilation and carbon assimilation, play an auxiliary role in regulation of starch synthesis, ATP production, peroxide detoxification, and participate in modulation of several other important biochemical pathways. Plant development and seed germination appear also to be under control of factors whose interaction with 14-3-3 molecules is crucial for their activation. Located within the nucleus, 14-3-3 isoforms are constituents of transcription factor complexes and interact with components of abscisic acid (ABA)-induced gene expression machinery. In addition, in animal cells they participate in nucleo-cytoplasmic trafficking and molecular sequestration. Cytoplasmic 14-3-3 members form a guidance complex with chloroplast destined preproteins and facilitate their import into these photosynthetic organelles. Recently, several 14-3-3s have been identified within chloroplasts where they could be involved in targeting and insertion of thylakoid proteins. The identification of 14-3-3 isoform specificity, and in particular the elucidation of the signal transduction mechanisms connecting 14-3-3 members with physiological responses, are central and developing topics of current research in this field.

Molecular sequestration stabilizes CAP-DNA complexes during polyacrylamide gel electrophoresis.

The gel electrophoresis mobility shift assay is widely used for qualitative and quantitative characterization of protein complexes with nucleic acids. Often it is found that complexes that are short-lived in free solution (t1/2 of the order of minutes) persist for hours under the conditions of gel electrophoresis. We have investigated the influence of polyacrylamide gels on the pseudo first-order dissociation kinetics of complexes containing the E.coli cyclic AMP receptor protein (CAP) and lactose promoter DNA. Within the gel matrix, kdiss decreased with increasing [polyacrylamide] and the order of the reaction was changed. In free solution, kdiss was proportional to [DNA]2, while in 5% gels, kdiss was proportional to [DNA]0.3. In gels of [polyacrylamide] > or = 10%, kdiss was nearly independent of [DNA] until fragment concentrations exceeded 0.1 microM. Even in the absence of competing DNA, kdiss(gel) < kdiss(solution). These results suggest that the lifetime of CAP-DNA complexes in free solution is limited by their encounter frequency with molecules of DNA or with protein-DNA complexes; some or all of the stabilization observed in gels may be due to a reduction in this frequency.