Insights into the mechanism of human erythrocyte hexose transport : a transferred NOE study of glucose binding to GLUT1

This study examines binding of α- and β-D-glucose in their equilibrium mixture to the glucose transporter (GLUT1) in human erythrocyte membrane preparations by an ^1H NMR method, the transferred NOE (TRNOE). This method is shown theoretically and experimentally to be a sensitive probe of weak ligand-macromolecule interactions. The TRNOEs observed are shown to arise solely from glucose binding to GLUT1. Sites at both membrane faces contribute to the TRNOEs. Binding curves obtained are consistent with a homogeneous class of sugar sites, with an apparent K_D which varies (from ~30 mM to ~70 mM for both anomers) depending on the membrane preparation examined. Preparations with a higher proportion of the cytoplasmic membrane face exposed to bulk solution yield higher apparent KK_Ds. The glucose transport inhibitor cytochalasin B essentially eliminates the TRNOE. Nonlinearity was found in the dependence on sugar concentration of the apparent inhibition constant for cytochalasin B reversal of the TRNOE observed in the α anomer (and probably the β anomer); such nonlinearity implies the existence of ternary complexes of sugar, inhibitor and transporter. The inhibition results furthermore imply the presence of a class of relatively high-affinity (K_D < 2mM) sugar sites specific for the α anomer which do not contribute to NMR-observable binding. The presence of two classes of sugar-sensitive cytochalasin B sites is also indicated. These results are compared with predictions of the alternating conformer model of glucose transport. Variation of apparent K_D in the NMR-observable sites, the formation of ternary complexes and the presence of an anomer-specific site are shown to be inconsistent with this model. An alternate model is developed which reconciles these results with the known transport behavior of GLUT1. In this model, the transporter possesses (at minimum) three classes of sugar sites: (i) transport sites, which are alternately exposed to the cytoplasmic or the extracellular compartment, but never to both simultaneously, (ii) a class of sites (probably relatively low-affinity) which are confined to one compartment, and (iii) the high-affinity α anomer-specific sites, which are confined to the cytoplasmic compartment.

Transport of pollutants through the water and subsurface soil using simulated acid rain

The mobility of heavy metals (Zn, Cd, Pb and Ni) was studied in the laboratory acidic leaching two different soils around Ibadan with simulated acid rain. The sampling was carried out from two different sites viz: Orogun and Ilupeju respectively. For Orogun site a depth of 128cm was reached (consisting of four horizons). Different length of polyvinyl chloride (PVC) pipes were cut for different soil horizon depth as observed on the field. The PVC pipes were packed with requires masses of soil. This is then leached using simulated acid rain of different pH of 2.0, 4.0, 6.0 and 8.0 after spiking with known volume of standard solution of metals of interest. It was found that simulated acid rain enhanced the mobility of metals in solution. The pH, Cation Exchange capacity, % clay and organic matter were found to contributed majority to the mobility of metals. Generally as observed, the mobility of metal was to follow the order Zn>Ni>Pb>Cd as the soil is becoming more acidic

The application of metallointercalators in recognition of and charge transport in nucleic acids

Metal complexes that utilize the 9,10-phenanthrene quinone diimine (phi) moiety bind to DNA through the major groove. These metallointercalators can recognize DNA sites and perform reactions on DNA as a substrate. The site-specific metallointercalator Λ-1-Rh(MGP)_2phi^(5+) competitively disrupts the major groove binding of a transcription factor, yAP-1, from an oligonucleotide that contains a common binding site. The demonstration that metal complexes can prevent transcription factor binding to DNA site-specifically is an important step in using metallointercalators as therapeutics.

The distinctive photochemistry of metallointercalators can also be applied to promote long range charge transport in DNA. Experiments using duplexes with regions 4 to 10 nucleotides long containing strictly adenine and thymine sequences of varying order showed that radical migration is more dependent on the sequence of bases, and less dependent on the distance between the guanine doublets. This result suggests that mechanistic proposals of long range charge transport must involve all the bases.

RNA/DNA hybrids show charge migration to guanines from a remote site, thus demonstrating that nucleic acid stacking other than B-form can serve as a radical bridge. Double crossover DNA assemblies also provide a medium for charge transport at distances up to 100 Å from the site of radical introduction by a tethered metal complex. This radical migration was found to be robust to mismatches, and limited to individual, electronically distinct base stacks. In single DNA crossover assemblies, which have considerably greater flexibility, charge migration proceeds to both base stacks due to conformational isomers not present in the rigid and tightly annealed double crossovers.

Finally, a rapid, efficient, gel-based technique was developed to investigate thymine dimer repair. Two oligonucleotides, one radioactively labeled, are photoligated via the bases of a thymine-thymine interface; reversal of this ligation is easily visualized by gel electrophoresis. This assay was used to show that the repair of thymine dimers from a distance through DNA charge transport can be accomplished with different photooxidants.

Thus, nucleic acids that support long range charge transport have been shown to include A-track DNA, RNA/DNA hybrids, and single and double crossovers, and a method for thymine dimer repair detection using charge transport was developed. These observations underscore and extend the remarkable finding that DNA can serve a medium for charge transport via the heteroaromatic base stack.

High temperature transport properties of lead chalcogenides and their alloys

This thesis describes a series of experimental studies of lead chalcogenide thermoelectric semiconductors, mainly PbSe. Focusing on a well-studied semiconductor and reporting good but not extraordinary zT, this thesis distinguishes itself by answering the following questions that haven’t been answered: What represents the thermoelectric performance of PbSe? Where does the high zT come from? How (and how much) can we make it better? For the first question, samples were made with highest quality. Each transport property was carefully measured, cross-verified and compared with both historical and contemporary report to overturn commonly believed underestimation of zT. For n- and p-type PbSe zT at 850 K can be 1.1 and 1.0, respectively. For the second question, a systematic approach of quality factor B was used. In n-type PbSe zT is benefited from its high-quality conduction band that combines good degeneracy, low band mass and low deformation potential, whereas zT of p-type is boosted when two mediocre valence bands converge (in band edge energy). In both cases the thermal conductivity from PbSe lattice is inherently low. For the third question, the use of solid solution lead chalcogenide alloys was first evaluated. Simple criteria were proposed to help quickly evaluate the potential of improving zT by introducing atomic disorder. For both PbTe1-xSex and PbSe1-xSx, the impacts in electron and phonon transport compensate each other. Thus, zT in each case was roughly the average of two binary compounds. In p-type Pb1-xSrxSe alloys an improvement of zT from 1.1 to 1.5 at 900 K was achieved, due to the band engineering effect that moves the two valence bands closer in energy. To date, making n-type PbSe better hasn’t been accomplished, but possible strategy is discussed.

Trends in Income and Price Elasticities of Transport Demand (1850-2010)

40 p.

Velocity resolved - scalar modeled simulations of high Schmidt number turbulent transport

The objective of this thesis is to develop a framework to conduct velocity resolved - scalar modeled (VR-SM) simulations, which will enable accurate simulations at higher Reynolds and Schmidt (Sc) numbers than are currently feasible. The framework established will serve as a first step to enable future simulation studies for practical applications. To achieve this goal, in-depth analyses of the physical, numerical, and modeling aspects related to Sc>>1 are presented, specifically when modeling in the viscous-convective subrange. Transport characteristics are scrutinized by examining scalar-velocity Fourier mode interactions in Direct Numerical Simulation (DNS) datasets and suggest that scalar modes in the viscous-convective subrange do not directly affect large-scale transport for high Sc. Further observations confirm that discretization errors inherent in numerical schemes can be sufficiently large to wipe out any meaningful contribution from subfilter models. This provides strong incentive to develop more effective numerical schemes to support high Sc simulations. To lower numerical dissipation while maintaining physically and mathematically appropriate scalar bounds during the convection step, a novel method of enforcing bounds is formulated, specifically for use with cubic Hermite polynomials. Boundedness of the scalar being transported is effected by applying derivative limiting techniques, and physically plausible single sub-cell extrema are allowed to exist to help minimize numerical dissipation. The proposed bounding algorithm results in significant performance gain in DNS of turbulent mixing layers and of homogeneous isotropic turbulence. Next, the combined physical/mathematical behavior of the subfilter scalar-flux vector is analyzed in homogeneous isotropic turbulence, by examining vector orientation in the strain-rate eigenframe. The results indicate no discernible dependence on the modeled scalar field, and lead to the identification of the tensor-diffusivity model as a good representation of the subfilter flux. Velocity resolved - scalar modeled simulations of homogeneous isotropic turbulence are conducted to confirm the behavior theorized in these a priori analyses, and suggest that the tensor-diffusivity model is ideal for use in the viscous-convective subrange. Simulations of a turbulent mixing layer are also discussed, with the partial objective of analyzing Schmidt number dependence of a variety of scalar statistics. Large-scale statistics are confirmed to be relatively independent of the Schmidt number for Sc>>1, which is explained by the dominance of subfilter dissipation over resolved molecular dissipation in the simulations. Overall, the VR-SM framework presented is quite effective in predicting large-scale transport characteristics of high Schmidt number scalars, however, it is determined that prediction of subfilter quantities would entail additional modeling intended specifically for this purpose. The VR-SM simulations presented in this thesis provide us with the opportunity to overlap with experimental studies, while at the same time creating an assortment of baseline datasets for future validation of LES models, thereby satisfying the objectives outlined for this work.

Band structure and transport properties of simple cubic tellurium-base alloys

The electrical transport properties and lattice spacings of simple cubic Te-Au, Te-Au-Fe, and Te-Au-Mn alloys, prepared by rapid quenching from the liquid state, hove been measured and correlated with a proposed bond structure. The variations of superconducting transition temperature, absolute thermoelectric power, and lattice spacing with Te concentration all showed related anomalies in the binary Te-Au alloys. The unusual behavior of these properties has been interpreted by using nearly free electron theory to predict the effect of the second Brillouin zone boundary on the area of the Fermi surface, and the electronic density of states. The behavior of the superconducting transition temperature and the lattice parameter as Fe and Mn ore added further supports the proposed interpretation as well as providing information on the existence of localized magnetic states in the ternary alloys. In addition, it was found that a very distinct bond structure effect on the transition temperatures of the Te-Au-Fe alloys could be identified.

A GIS-based model of soil erosion and transport

Soil erosion is a natural process that occurs when the force of wind, raindrops or running water on the soil surface exceeds the cohesive forces that bind the soil together. In general, vegetation cover protects the soil from the effects of these erosive forces. However, land management activities such as ploughing, burning or heavy grazing may disturb this protective layer, exposing the underlying soil. The decision making process in rural catchment management is often supported by the predictive modelling of soil erosion and sediment transport processes within the catchment, using established techniques such as the Universal Soil Loss Equation [USLE] and the Agricultural Nonpoint Source pollution model [AGNPS]. In this article, the authors examine the range of erosion models currently available and describe the application of one of these to the Burrishoole catchment on the north-west coast of Ireland, which has suffered heavy erosion of blanket peat in recent years.

Factors influencing the downstream transport of sediment in the Lough Feeagh catchment, Burrishoole, Co. Mayo, Ireland

Research laboratories in the Burrishoole catchment have been the focus of salmonid research since 1955. One aspect of the research has been to monitor the number of salmon and sea trout migrating to sea as smolts and returning to the catchment as adults. In the early 1990s it became clear that the smolt output from the catchment had declined over the previous two decades. At about the same time the presence of fine particles of peat silt in the hatchery became increasingly apparent and led to a higher incidence of mortality of young fry. These observations and management difficulties led to a study of silt transport in the surface waters of the catchment, which is described in this article. The authors describe geology, soils, climate and hydrology of Burrishoole before examining the sediment deposition in Lough Feeagh.

Modelling soil erosion and transport in the Burrishoole catchment, Newport, Co. Mayo, Ireland

The Burrishoole catchment is situated in County Mayo, on the northwest coast of the Republic of Ireland. Much of the catchment is covered by blanket peat that, in many areas, has become heavily eroded in recent years. This is thought to be due, primarily, to the adverse effects of forestry and agricultural activities in the area. Such activities include ploughing, drainage, the planting and harvesting of trees, and sheep farming, all of which are potentially damaging to such a sensitive landscape if not managed carefully. This article examines the sediment yield and hydrology of the Burrishoole catchment. Flow and sediment concentrations were measured at 8-hourly intervals from 5 February 2001 to 8 November 2001 with an automatic sampler and separate flow gauge, and hourly averages were recorded between 4 July 2002 and 6 September 2002 using an automatic river monitoring system [ARMS]. The authors describe the GIS-based model of soil erosion and transport that was applied to the Burrishoole catchment during this study. The results of these analyses were compared, in a qualitative manner, with the aerial photography available for the Burrishoole catchment to see whether areas that were predicted to contribute large proportions of eroded material to the drainage network corresponded with areas where peat erosion could be identified through photo-interpretation.

The transport of aquatic animals by birds. [Translation from: Binnengewaesser 18, 156-159, 1950.]

A great deal has been written on the part which birds play in the dispersal of freshwater fauna. This article summarises literature on the dispersal of aquatic animals by birds and aquatic insects.

DNA-Mediated Charge Transport Devices for Protein Detection

Detection of biologically relevant targets, including small molecules, proteins, DNA, and RNA, is vital for fundamental research as well as clinical diagnostics. Sensors with biological elements provide a natural foundation for such devices because of the inherent recognition capabilities of biomolecules. Electrochemical DNA platforms are simple, sensitive, and do not require complex target labeling or expensive instrumentation. Sensitivity and specificity are added to DNA electrochemical platforms when the physical properties of DNA are harnessed. The inherent structure of DNA, with its stacked core of aromatic bases, enables DNA to act as a wire via DNA-mediated charge transport (DNA CT). DNA CT is not only robust over long molecular distances of at least 34 nm, but is also especially sensitive to anything that perturbs proper base stacking, including DNA mismatches, lesions, or DNA-binding proteins that distort the π-stack. Electrochemical sensors based on DNA CT have previously been used for single-nucleotide polymorphism detection, hybridization assays, and DNA-binding protein detection. Here, improvements to (i) the structure of DNA monolayers and (ii) the signal amplification with DNA CT platforms for improved sensitivity and detection are described.

First, improvements to the control over DNA monolayer formation are reported through the incorporation of copper-free click chemistry into DNA monolayer assembly. As opposed to conventional film formation involving the self-assembly of thiolated DNA, copper-free click chemistry enables DNA to be tethered to a pre-formed mixed alkylthiol monolayer. The total amount of DNA in the final film is directly related to the amount of azide in the underlying alkylthiol monolayer. DNA monolayers formed with this technique are significantly more homogeneous and lower density, with a larger amount of individual helices exposed to the analyte solution. With these improved monolayers, significantly more sensitive detection of the transcription factor TATA binding protein (TBP) is achieved.

Using low-density DNA monolayers, two-electrode DNA arrays were designed and fabricated to enable the placement of multiple DNA sequences onto a single underlying electrode. To pattern DNA onto the primary electrode surface of these arrays, a copper precatalyst for click chemistry was electrochemically activated at the secondary electrode. The location of the secondary electrode relative to the primary electrode enabled the patterning of up to four sequences of DNA onto a single electrode surface. As opposed to conventional electrochemical readout from the primary, DNA-modified electrode, a secondary microelectrode, coupled with electrocatalytic signal amplification, enables more sensitive detection with spatial resolution on the DNA array electrode surface. Using this two-electrode platform, arrays have been formed that facilitate differentiation between well-matched and mismatched sequences, detection of transcription factors, and sequence-selective DNA hybridization, all with the incorporation of internal controls.

For effective clinical detection, the two working electrode platform was multiplexed to contain two complementary arrays, each with fifteen electrodes. This platform, coupled with low density DNA monolayers and electrocatalysis with readout from a secondary electrode, enabled even more sensitive detection from especially small volumes (4 μL per well). This multiplexed platform has enabled the simultaneous detection of two transcription factors, TBP and CopG, with surface dissociation constants comparable to their solution dissociation constants.

With the sensitivity and selectivity obtained from the multiplexed, two working electrode array, an electrochemical signal-on assay for activity of the human methyltransferase DNMT1 was incorporated. DNMT1 is the most abundant human methyltransferase, and its aberrant methylation has been linked to the development of cancer. However, current methods to monitor methyltransferase activity are either ineffective with crude samples or are impractical to develop for clinical applications due to a reliance on radioactivity. Electrochemical detection of methyltransferase activity, in contrast, circumvents these issues. The signal-on detection assay translates methylation events into electrochemical signals via a methylation-specific restriction enzyme. Using the two working electrode platform combined with this assay, DNMT1 activity from tumor and healthy adjacent tissue lysate were evaluated. Our electrochemical measurements revealed significant differences in methyltransferase activity between tumor tissue and healthy adjacent tissue.

As differential activity was observed between colorectal tumor tissue and healthy adjacent tissue, ten tumor sets were subsequently analyzed for DNMT1 activity both electrochemically and by tritium incorporation. These results were compared to expression levels of DNMT1, measured by qPCR, and total DNMT1 protein content, measured by Western blot. The only trend detected was that hyperactivity was observed in the tumor samples as compared to the healthy adjacent tissue when measured electrochemically. These advances in DNA CT-based platforms have propelled this class of sensors from the purely academic realm into the realm of clinically relevant detection.

A simple method for counting bacteria with active electron transport system in water and sediment samples [Translation from: Kiel. Meeresforsch. 31(2) 83-86, 1975]

Description of a simple method for counting bacteria with active electron transport systems in water and sediment samples. Sodium succinate, NADH and NADPH served as electron donors. It is possible to see several sites of electron transport in the larger cells. Especially impressive are the plankton-algae, protozoa, and small metazoa. This is a partial translation of the ”method” section only.

DNA-mediated charge transport signaling within the cell

DNA possesses the curious ability to conduct charge longitudinally through the π-stacked base pairs that reside within the interior of the double helix. The rate of charge transport (CT) through DNA has a shallow distance dependence. DNA CT can occur over at least 34 nm, a very long molecular distance. Lastly, DNA CT is exquisitely sensitive to disruptions, such as DNA damage, that affect the dynamics of base-pair stacking. Many DNA repair and DNA-processing enzymes are being found to contain 4Fe-4S clusters. These co-factors have been found in glycosylases, helicases, helicase-nucleases, and even enzymes such as DNA polymerase, RNA polymerase, and primase across the phylogeny. The role of these clusters in these enzymes has remained elusive. Generally, iron-sulfur clusters serve redox roles in nature since, formally, the cluster can exist in multiple oxidation states that can be accessed within a biological context. Taken together, these facts were used as a foundation for the hypothesis that DNA-binding proteins with 4Fe-4S clusters utilize DNA-mediated CT as a means to signal one another to scan the genome as a first step in locating the subtle damage that occurs within a sea of undamaged bases within cells.

Herein we describe a role for 4Fe-4S clusters in DNA-mediated charge transport signaling among EndoIII, MutY, and DinG, which are from distinct repair pathways in E. coli. The DinG helicase is an ATP-dependent helicase that contains a 4Fe-4S cluster. To study the DNA-bound redox properties of DinG, DNA-modified electrochemistry was used to show that the 4Fe-4S cluster of DNA-bound DinG is redox-active at cellular potentials, and shares the 80 mV vs. NHE redox potential of EndoIII and MutY. ATP hydrolysis by DinG increases the DNA-mediated redox signal observed electrochemically, likely reflecting better coupling of the 4Fe-4S cluster to DNA while DinG unwinds DNA, which could have interesting biological implications. Atomic force microscopy experiments demonstrate that DinG and EndoIII cooperate at long range using DNA charge transport to redistribute to regions of DNA damage. Genetics experiments, moreover, reveal that this DNA-mediated signaling among proteins also occurs within the cell and, remarkably, is required for cellular viability under conditions of stress. Knocking out DinG in CC104 cells leads to a decrease in MutY activity that is rescued by EndoIII D138A, but not EndoIII Y82A. DinG, thus, appears to help MutY find its substrate using DNA-mediated CT, but do MutY or EndoIII aid DinG in a similar way? The InvA strain of bacteria was used to observe DinG activity, since DinG activity is required within InvA to maintain normal growth. Silencing the gene encoding EndoIII in InvA results in a significant growth defect that is rescued by the overexpression of RNAseH, a protein that dismantles the substrate of DinG, R-loops. This establishes signaling between DinG and EndoIII. Furthermore, rescue of this growth defect by the expression of EndoIII D138A, the catalytically inactive but CT-proficient mutant of EndoIII, is also observed, but expression of EndoIII Y82A, which is CT-deficient but enzymatically active, does not rescue growth. These results provide strong evidence that DinG and EndoIII utilize DNA-mediated signaling to process DNA damage. This work thus expands the scope of DNA-mediated signaling within the cell, as it indicates that DNA-mediated signaling facilitates the activities of DNA repair enzymes across the genome, even for proteins from distinct repair pathways.

In separate work presented here, it is shown that the UvrC protein from E. coli contains a hitherto undiscovered 4Fe-4S cluster. A broad shoulder at 410 nm, characteristic of 4Fe-4S clusters, is observed in the UV-visible absorbance spectrum of UvrC. Electron paramagnetic resonance spectroscopy of UvrC incubated with sodium dithionite, reveals a spectrum with the signature features of a reduced, [4Fe-4S]+1, cluster. DNA-modified electrodes were used to show that UvrC has the same DNA-bound redox potential, of ~80 mV vs. NHE, as EndoIII, DinG, and MutY. Again, this means that these proteins are capable of performing inter-protein electron transfer reactions. Does UvrC use DNA-mediated signaling to facilitate the repair of its substrates?

UvrC is part of the nucleotide excision repair (NER) pathway in E. coli and is the protein within the pathway that performs the chemistry required to repair bulky DNA lesions, such as cyclopyrimidine dimers, that form as a product of UV irradiation. We tested if UvrC utilizes DNA-mediated signaling to facilitate the efficient repair of UV-induced DNA damage products by helping UvrC locate DNA damage. The UV sensitivity of E. coli cells lacking DinG, a putative signaling partner of UvrC, was examined. Knocking out DinG in E. coli leads to a sensitivity of the cells to UV irradiation. A 5-10 fold reduction in the amount of cells that survive after irradiation with 90 J/m2 of UV light is observed. This is consistent with the hypothesis that UvrC and DinG are signaling partners, but is this signaling due to DNA-mediated CT? Complementing the knockout cells with EndoIII D138A, which can also serve as a DNA CT signaling partner, rescues cells lacking DinG from UV irradiation, while complementing the cells with EndoIII Y82A shows no rescue of viability. These results indicate that there is cross-talk between the NER pathway and DinG via DNA-mediated signaling. Perhaps more importantly, this work also establishes that DinG, EndoIII, MutY, and UvrC comprise a signaling network that seems to be unified by the ability of these proteins to perform long range DNA-mediated CT signaling via their 4Fe-4S clusters.