ResearchPad - material-properties Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Insight into the protein solubility driving forces with neural attention]]> The solubility of proteins is a crucial biophysical aspect when it comes to understanding many human diseases and to improve the industrial processes for protein production. Due to its relevance, computational methods have been devised in order to study and possibly optimize the solubility of proteins. In this work we apply a deep-learning technique, called neural attention to predict protein solubility while “opening” the model itself to interpretability, even though Machine Learning models are usually considered black boxes. Thank to the attention mechanism, we show that i) our model implicitly learns complex patterns related to emergent, protein folding-related, aspects such as to recognize β-amyloidosis regions and that ii) the N-and C-termini are the regions with the highes signal fro solubility prediction. When it comes to enhancing the solubility of proteins, we, for the first time, propose to investigate the synergistic effects of tandem mutations instead of “single” mutations, suggesting that this could minimize the number of required proposed mutations.

<![CDATA[Mechanical characterization of PVA hydrogels’ rate-dependent response using multi-axial loading]]> The time-dependent properties of rubber-like synthesized and biological materials are crucial for their applications. Currently, this behavior is mainly measured using axial tensile test, compression test, or indentation. Limited studies performed on using multi-axial loading measurements of time-dependent material behavior exist in the literature. Therefore, the aim of this study is to investigate the viscoelastic response of rubber-like materials under multi-axial loading using cavity expansion and relaxation tests. The tests were performed on PVA hydrogel specimens. Three hyperelasitc models and one term Prony series were used to characterize the viscoelastic response of the hydrogels. Finite element (FE) simulations were performed to verify the validity of the calibrated material coefficients by reproducing the experimental results. The excellent agreement between the experimental, analytical and numerical data proves the capability of the cavity expansion technique to measure the time-dependent behavior of viscoelastic materials.

<![CDATA[Instigation of indigenous thermophilic bacterial consortia for enhanced oil recovery from high temperature oil reservoirs]]> The purpose of the study involves the development of an anaerobic, thermophilic microbial consortium TERIK from the high temperature reservoir of Gujarat for enhance oil recovery. To isolate indigenous microbial consortia, anaerobic baltch media were prepared and inoculated with the formation water; incubated at 65°C for 10 days. Further, the microbial metabolites were analyzed by gas chromatography, FTIR and surface tension. The efficiency of isolated consortia towards enhancing oil recovery was analyzed through core flood assay. The novelty of studied consortia was that, it produces biomass (600 mg/l), bio-surfactant (325 mg/l), and volatile fatty acids (250 mg/l) at 65°C in the span of 10 days, that are adequate to alter the surface tension (70 to 34 mNm -1) and sweep efficiency of zones facilitating the displacement of oil. TERIK was identified as Clostridium sp. The FTIR spectra of biosurfactant indicate the presence of N-H stretch, amides and polysaccharide. A core flooding assay was designed to explore the potential of TERIK towards enhancing oil recovery. The results showed an effective reduction in permeability at residual oil saturation from 2.14 ± 0.1 to 1.39 ± 0.05 mD and 19% incremental oil recovery.

<![CDATA[Effect of experimental, morphological and mechanical factors on the murine spinal cord subjected to transverse contusion: A finite element study]]> Finite element models combined with animal experimental models of spinal cord injury provides the opportunity for investigating the effects of the injury mechanism on the neural tissue deformation and the resulting tissue damage. Thus, we developed a finite element model of the mouse cervical spinal cord in order to investigate the effect of morphological, experimental and mechanical factors on the spinal cord mechanical behavior subjected to transverse contusion. The overall mechanical behavior of the model was validated with experimental data of unilateral cervical contusion in mice. The effects of the spinal cord material properties, diameter and curvature, and of the impactor position and inclination on the strain distribution were investigated in 8 spinal cord anatomical regions of interest for 98 configurations of the model. Pareto analysis revealed that the material properties had a significant effect (p<0.01) for all regions of interest of the spinal cord and was the most influential factor for 7 out of 8 regions. This highlighted the need for comprehensive mechanical characterization of the gray and white matter in order to develop effective models capable of predicting tissue deformation during spinal cord injuries.

<![CDATA[The natural drug DIAVIT is protective in a type II mouse model of diabetic nephropathy]]>

There is evidence to suggest that abnormal angiogenesis, inflammation, and fibrosis drive diabetic nephropathy (DN). However, there is no specific treatment to counteract these processes. We aimed to determine whether DIAVIT, a natural Vaccinium myrtillus (blueberry) and Hippophae Rhamnoides (sea buckthorn) extract, is protective in a model of type II DN. Diabetic db/db mice were administered DIAVIT in their drinking water for 14 weeks. We assessed the functional, structural, and ultra-structural phenotype of three experimental groups (lean+vehicle, db/db+vehicle, db/db+DIAVIT). We also investigated the angiogenic and fibrotic pathways involved in the mechanism of action of DIAVIT. Diabetic db/db mice developed hyperglycaemia, albuminuria, and an increased glomerular water permeability; the latter two were prevented by DIAVIT. db/db mice developed fibrotic glomeruli, endothelial insult, and glomerular ultra-structural changes, which were not present in DIAVIT-treated mice. Vascular endothelial growth factor A (VEGF-A) splicing was altered in the db/db kidney cortex, increasing the pro-angiogenic VEGF-A165 relative to the anti-angiogenic VEGF-A165b. This was partially prevented with DIAVIT treatment. Delphinidin, an anthocyanin abundant in DIAVIT, increased the VEGF-A165b expression relative to total VEGF-A165 in cultured podocytes through phosphorylation of the splice factor SRSF6. DIAVIT, in particular delphinidin, alters VEGF-A splicing in type II DN, rescuing the DN phenotype. This study highlights the therapeutic potential of natural drugs in DN through the manipulation of gene splicing and expression.

<![CDATA[The effect of Mn2Sb2 and Mn2Sb secondary phases on magnetism in (GaMn)Sb thin films]]>

In this work, a detailed study of structural, electrical and magnetic characterization of (GaMn)Sb diluted magnetic semiconductors (DMS) is presented. (GaMn)Sb thin films were grown by DC magnetron co-sputtering method as an innovative procedure to fabricate III-V DMS. The presence of unusual Mn2Sb2 and Mn2Sb secondary phases, induced by substrate temperature and deposition time, were revealed through XRD measurements. Magnetization measurements allow determining crossover between a paramagnetic-like to a ferromagnetic-like behavior controlled by secondary phases. It was found that both, the magnetic remanence and magnetic coercivity, increases with substrate temperature. Interestingly, the magnetic response is paramagnetic at lower deposition times and substrate temperatures, and XRD measurements suggest the absence of Mn2Sb and Mn2Sb2 in secondary phases. For longer deposition times or higher substrate temperature, XRD shows the presence of Mn2Sb2 and Mn2Sb phases and ferromagnetic-like behavior. The DC resistivity of our samples was characterized and the carrier density was determined by Hall measurements and, in contrast with the reported in other studies, found them to be a p-type semiconductor with carrier densities as big as one order of magnitude larger than reported values. From the ferromagnetic-like samples, evidence of an anomalous Hall-effect in the sample was found, with higher magnetic saturation and a anomalous Hall conductivity of 2380 S/cm. All the results point to a contribution of the secondary phases to the overall magnetic response of the samples used, and suggest the importance of studying the formation of secondary phases in the growth of DMS, especially, for the case of (GaMn)Sb where Mn ion can have multiple oxidation states.

<![CDATA[Effect of internal surface structure of the north wall on Chinese solar greenhouse thermal microclimate based on computational fluid dynamics]]>

Chinese solar greenhouses are unique facility agriculture buildings and widely used in northeastern China, providing a favorable requirement for crop growth. The north wall configurations play an essential role in heat storage and thermal insulation and directly affect the management of the internal environment. This research is devoted to further improve the thermal performance of the greenhouse and explore the potential of the north wall. A mathematical model was designed to investigate the concave-convex wall configurations based on computational fluid dynamics. Four passive heat-storage north walls were analyzed by using the same constituent materials, including a plane wall, a vertical wall, a horizontal wall and an alveolate wall. The numerical model was validated by experimental measurements. The temperature distributions of the north walls were examined and a comparative analysis of the heat storage-release capabilities was carried out. The results showed that the heat-storage capacity of the north wall is affected by the surface structure. Moreover, the critical factor influencing the air temperature is the sum of the heat load released by the wall and the energy increment of greenhouse air. The results suggested that the alveolate wall has preferable thermal accumulation capacity. The concave-convex wall configurations have a wider range of heat transfer performance along the thickness direction, while the plane wall has a superior thermal environment. This study provides a basic theoretical reference to rationally design the internal surface structures of the north wall.

<![CDATA[Assessing the effects of intratendinous genipin injections: Mechanical augmentation and spatial distribution in an ex vivo degenerative tendon model]]>


Tendinopathy is a common musculoskeletal disorder and current treatment options show limited success. Genipin is an effective collagen crosslinker with low cytotoxicity and a promising therapeutic strategy for stabilizing an intratendinous lesion.


This study examined the mechanical effect and delivery of intratendinous genipin injection in healthy and degenerated tendons.

Study design

Controlled laboratory study


Bovine superficial digital flexor tendons were randomized into four groups: Healthy control (N = 25), healthy genipin (N = 25), degenerated control (N = 45) and degenerated genipin (N = 45). Degeneration was induced by Collagenase D injection. After 24h, degenerated tendons were subsequently injected with either 0.2ml of 80mM genipin or buffer only. 24h post-treatment, samples were cyclically loaded for 500 cycles and then ramp loaded to failure. Fluorescence and absorption assays were performed to analyze genipin crosslink distribution and estimate tissue concentration after injection.


Compared to controls, genipin treatment increased ultimate force by 19% in degenerated tendons (median control 530 N vs. 633 N; p = 0.0078). No significant differences in mechanical properties were observed in healthy tendons, while degenerated tendons showed a significant difference in ultimate stress (+23%, p = 0.049), stiffness (+27%, p = 0.037), work to failure (+42%, p = 0.009), and relative stress relaxation (-11%, p < 0.001) after genipin injection. Fluorescence and absorption were significantly higher in genipin treated tendons compared to control groups. A higher degree of crosslinking (+45%, p < 0.001) and a more localized distribution were observed in the treated healthy compared to degenerated tendons, with higher genipin tissue concentrations in healthy (7.9 mM) than in degenerated tissue (2.3 mM).


Using an ex-vivo tendinopathy model, intratendinous genipin injections recovered mechanical strength to the level of healthy tendons. Measured by genipin tissue distribution, injection is an effective method for local delivery.

Clinical relevance

This study provides a proof of concept for the use of intratendinous genipin injection in the treatment of tendinopathy. The results demonstrate that a degenerated tendon can be mechanically augmented by a clinically viable method of local genipin delivery. This warrants further in vivo studies towards the development of a clinically applicable treatment based on genipin.

<![CDATA[Analysis on hydraulic characteristics of improved sandy soil with soft rock]]>

Hydraulic properties of sandy soil from the Mu Us sandy land of Shaanxi Province were analyzed by using SEM technology. Soil porosity, the water characteristic curve, and unsaturated hydraulic conductivity of aeolian sandy soil with added soft rock were analyzed, and fractal characteristics were established. Soil hydraulic properties revealed the effect of soft rock application on soil structure and hydraulic properties. Mass ratios of soft rock to aeolian sand were 1:5, 1:2, and 1:1. Results showed that the addition of soft rock can significantly increase the bulk density of sandy soil and reduce the total porosity and macroporosity. The mass fraction of water-stable aggregates greater than 0.25mm increases significantly, increasing the fractal dimension of soil pores; reducing the soil saturated water content and saturated hydraulic conductivity. SEM technology and pore fractal theory were used to predict the soil salinity curve and unsaturated hydraulic conductivity of the improved saline soil.

<![CDATA[A new finite element based parameter to predict bone fracture]]>

Dual Energy X-Ray Absorptiometry (DXA) is currently the most widely adopted non-invasive clinical technique to assess bone mineral density and bone mineral content in human research and represents the primary tool for the diagnosis of osteoporosis. DXA measures areal bone mineral density, BMD, which does not account for the three-dimensional structure of the vertebrae and for the distribution of bone mass. The result is that longitudinal DXA can only predict about 70% of vertebral fractures. This study proposes a complementary tool, based on Finite Element (FE) models, to improve the DXA accuracy. Bone is simulated as elastic and inhomogeneous material, with stiffness distribution derived from DXA greyscale images of density. The numerical procedure simulates a compressive load on each vertebra to evaluate the local minimum principal strain values. From these values, both the local average and the maximum strains are computed over the cross sections and along the height of the analysed bone region, to provide a parameter, named Strain Index of Bone (SIB), which could be considered as a bone fragility index. The procedure is initially validated on 33 cylindrical trabecular bone samples obtained from porcine lumbar vertebrae, experimentally tested under static compressive loading. Comparing the experimental mechanical parameters with the SIB, we could find a higher correlation of the ultimate stress, σULT, with the SIB values (R2adj = 0.63) than that observed with the conventional DXA-based clinical parameters, i.e. Bone Mineral Density, BMD (R2adj = 0.34) and Trabecular Bone Score, TBS (R2adj = -0.03). The paper finally presents a few case studies of numerical simulations carried out on human lumbar vertebrae. If our results are confirmed in prospective studies, SIB could be used—together with BMD and TBS—to improve the fracture risk assessment and support the clinical decision to assume specific drugs for metabolic bone diseases.

<![CDATA[Graphene oxide in zinc alginate films: Antibacterial activity, cytotoxicity, zinc release, water sorption/diffusion, wettability and opacity]]>

Alginate is considered an exceptional biomaterial due to its hydrophilicity, biocompatibility, biodegradability, nontoxicity and low-cost in comparison with other biopolymers. We have recently demonstrated that the incorporation of 1% graphene oxide (GO) into alginate films crosslinked with Ca2+ cations provides antibacterial activity against Staphylococcus aureus and methicillin-resistant Staphylococcus epidermidis, and no cytotoxicity for human keratinocyte HaCaT cells. However, many other reports in literature have shown controversial results about the toxicity of GO demanding further investigation. Furthermore, the synergic effect of GO with other divalent cations with intrinsic antibacterial and cytotoxic activity such as Zn2+ has not been explored yet. Thus, here, two commercially available sodium alginates were characterised and utilized in the synthesis of zinc alginate films with GO following the same chemical route reported for the calcium alginate/GO composites. The results of this study showed that zinc release, water sorption/diffusion and wettability depended significantly on the type of alginate utilized. Furthermore, Zn2+ and GO produced alginate films with increased water diffusion, wettability and opacity. However, neither the combination of GO with Zn2+ nor the use of different types of sodium alginates modified the antibacterial activity and cytotoxicity of the zinc alginates against these Gram-positive pathogens and human cells respectively.

<![CDATA[Probabilistic analysis of a concrete column in an aggressive soil environment]]>

Sulphate attack is one of the most important factors that limit the lifetime of pure concrete constructions. Harsh environmental conditions have a large impact on the operational costs of concrete columns or piles dipped into soil. The results are non-deterministic; therefore, reliability analysis is often used. The strength characteristics of the substrate around the construction were modelled as one-dimensional prismatic beams related with random p-y curves. Sulphate deterioration is defined as a set of random variables jointed with two dimensional mechanical systems at acceptable levels. Fick’s second law describes the penetration of sulphate ingress into pure concrete with explicit numerical solutions for boundary conditions and an increase in the transition factor under the progress of sulphate ingress. This process was partially solved via analytical methods for sulphate ion transport and numerically for a random field. This solves the mechanical task and determines the system reliability. A numerical example is provided to illustrate the proposed method to prevent unexpected structural failures during column service life. The proposed methodology can assist designers and can help to make decisions on existing foundations to ensure the safety of geotechnical construction.

<![CDATA[Molecular mechanisms of mesoporous silica formation from colloid solution: Ripening-reactions arrest hollow network structures]]>

The agglomeration of silica nanoparticles in aqueous solution is investigated from molecular simulations. Mimicking destabilization of colloidal solutions by full removal of protective moieties or surface charge, association of SiO2/Si(OH)4 core/shell particles leads to rapid proton transfer reactions that account for local silanole → silica ripening reactions. Yet, such virtually barrier-less binding is only observed within a limited contact zone. Agglomeration hence leads to the formation of oligomers of nanoparticles, whilst full merging into a compact precipitate is hampered by the need for extended structural reorganisation. Implementing sufficiently fast supply from colloidal solution, our simulations show the development of silica networks comprised of covalently bound, yet not fully merged nanoparticles. Within the oligomerized nanoparticle network, coordination numbers range from 2 to 5 –which is far below closest packing. Our simulations hence rationalize the formation of covalently bound network structures hosting extended pores. The resulting interfaces to the solvent show water immobilization only for the immediate contact layers, whilst the inner pores exhibit solvent mobility akin to bulk water.

<![CDATA[In-silico pre-clinical trials are made possible by a new simple and comprehensive lumbar belt mechanical model based on the Law of Laplace including support deformation and adhesion effects]]>

Lower back pain is a major public health problem. Despite claims that lumbar belts change spinal posture due to applied pressure on the trunk, no mechanical model has yet been published to prove this treatment. This paper describes a first model for belt design, based on the one hand on the mechanical properties of the fabrics and the belt geometry, and on the other hand on the trunk geometrical and mechanical description. The model provides the estimation of the pressure applied to the trunk, and a unique indicator of the belt mechanical efficiency is proposed: pressure is integrated into a bending moment characterizing the belt delordosing action on the spine. A first in-silico clinical study of belt efficiency for 15 patients with 2 different belts was conducted. Results are very dependent on the body shape: in the case of high BMI patients, the belt effect is significantly decreased, and can be even inverted, increasing the lordosis. The belt stiffness proportionally increases the pressure applied to the trunk, but the influence of the design itself on the bending moment is clearly outlined. Moreover, the belt/trunk interaction, modeled as sticking contact and the specific way patients lock their belts, dramatically modifies the belt action. Finally, even if further developments and tests are still necessary, the model presented in this paper seems suitable for in-silico pre-clinical trials on real body shapes at a design stage.

<![CDATA[Postural control of a musculoskeletal model against multidirectional support surface translations]]>

The human body is a complex system driven by hundreds of muscles, and its control mechanisms are not sufficiently understood. To understand the mechanisms of human postural control, neural controller models have been proposed by different research groups, including our feed-forward and feedback control model. However, these models have been evaluated under forward and backward perturbations, at most. Because a human body experiences perturbations from many different directions in daily life, neural controller models should be evaluated in response to multidirectional perturbations, including in the forward/backward, lateral, and diagonal directions. The objective of this study was to investigate the validity of an NC model with FF and FB control under multidirectional perturbations. We developed a musculoskeletal model with 70 muscles and 15 degrees of freedom of joints, positioned it in a standing posture by using the neural controller model, and translated its support surface in multiple directions as perturbations. We successfully determined the parameters of the neural controller model required to maintain the stance of the musculoskeletal model for each perturbation direction. The trends in muscle response magnitudes and the magnitude of passive ankle stiffness were consistent with the results of experimental studies. We conclude that the neural controller model can adapt to multidirectional perturbations by generating suitable muscle activations. We anticipate that the neural controller model could be applied to the study of the control mechanisms of patients with torso tilt and diagnosis of the change in control mechanisms from patients’ behaviors.

<![CDATA[Detailed characterization of the solution kinetics and thermodynamics of biotin, biocytin and HABA binding to avidin and streptavidin]]>

The high affinity (KD ~ 10−15 M) of biotin for avidin and streptavidin is the essential component in a multitude of bioassays with many experiments using biotin modifications to invoke coupling. Equilibration times suggested for these assays assume that the association rate constant (kon) is approximately diffusion limited (109 M-1s-1) but recent single molecule and surface binding studies indicate that they are slower than expected (105 to 107 M-1s-1). In this study, we asked whether these reactions in solution are diffusion controlled, which reaction model and thermodynamic cycle describes the complex formation, and if there are any functional differences between avidin and streptavidin. We have studied the biotin association by two stopped-flow methodologies using labeled and unlabeled probes: I) fluorescent probes attached to biotin and biocytin; and II) unlabeled biotin and HABA, 2-(4’-hydroxyazobenzene)-benzoic acid. Both native avidin and streptavidin are homo-tetrameric and the association data show no cooperativity between the binding sites. The kon values of streptavidin are faster than avidin but slower than expected for a diffusion limited reaction in both complexes. Moreover, the Arrhenius plots of the kon values revealed strong temperature dependence with large activation energies (6–15 kcal/mol) that do not correspond to a diffusion limited process (3–4 kcal/mol). Accordingly, we propose a simple reaction model with a single transition state for non-immobilized reactants whose forward thermodynamic parameters complete the thermodynamic cycle, in agreement with previously reported studies. Our new understanding and description of the kinetics, thermodynamics, and spectroscopic parameters for these complexes will help to improve purification efficiencies, molecule detection, and drug screening assays or find new applications.

<![CDATA[Population dynamics and socio-spatial organization of the Aurignacian: Scalable quantitative demographic data for western and central Europe]]>

Demographic estimates are presented for the Aurignacian techno-complex (~42,000 to 33,000 y calBP) and discussed in the context of socio-spatial organization of hunter-gatherer populations. Results of the analytical approach applied estimate a mean of 1,500 persons (upper limit: 3,300; lower limit: 800) for western and central Europe. The temporal and spatial analysis indicates an increase of the population during the Aurignacian as well as marked regional differences in population size and density. Demographic increase and patterns of socio-spatial organization continue during the subsequent early Gravettian period. We introduce the concept of Core Areas and Extended Areas as informed analytical spatial scales, which are evaluated against additional chronological and archaeological data. Lithic raw material transport and personal ornaments serve as correlates for human mobility and connectedness in the interpretative framework of this study. Observed regional differences are set in relation with the new demographic data. Our large-scale approach on Aurignacian population dynamics in Europe suggests that past socio-spatial organization followed socially inherent rules to establish and maintain a functioning social network of extremely low population densities. The data suggest that the network was fully established across Europe during the early phase of the Gravettian, when demographic as well as cultural developments peaked.

<![CDATA[A low-cost, autonomous mobile platform for limnological investigations, supported by high-resolution mesoscale airborne imagery]]>

Two complementary measurement systems—built upon an autonomous floating craft and a tethered balloon—for lake research and monitoring are presented. The autonomous vehicle was assembled on a catamaran for stability, and is capable of handling a variety of instrumentation for in situ and near-surface measurements. The catamaran hulls, each equipped with a small electric motor, support rigid decks for arranging equipment. An electric generator provides full autonomy for about 8 h. The modular power supply and instrumentation data management systems are housed in two boxes, which enable rapid setup. Due to legal restrictions in Switzerland (where the craft is routinely used), the platform must be observed from an accompanying boat while in operation. Nevertheless, the control system permits fully autonomous operation, with motion controlled by speed settings and waypoints, as well as obstacle detection. On-board instrumentation is connected to a central hub for data storage, with real-time monitoring of measurements from the accompanying boat. Measurements from the floating platform are complemented by mesoscale imaging from an instrument package attached to a He-filled balloon. The aerial package records thermal and RGB imagery, and transmits it in real-time to a ground station. The balloon can be tethered to the autonomous catamaran or to the accompanying boat. Missions can be modified according to imagery and/or catamaran measurements. Illustrative results showing the surface thermal variations of Lake Geneva demonstrate the versatility of the combined floating platform/balloon imagery system setup for limnological investigations.

<![CDATA[Iron influence on dissolved color in lakes of the Upper Great Lakes States]]>

Colored dissolved organic matter (CDOM), a major component of the dissolved organic carbon (DOC) pool in many lakes, is an important controlling factor in lake ecosystem functioning. Absorption coefficients at 440 nm (a440, m-1), a common measure of CDOM, exhibited strong associations with dissolved iron (Fediss) and DOC in 280 lakes of the Upper Great Lakes States (UGLS: Minnesota, Wisconsin, and Michigan), as has been found in Scandinavia and elsewhere. Linear regressions between the three variables on UGLS lake data typically yielded R2 values of 0.6–0.9, suggesting that some underlying common processes influence organic matter and Fediss. Statistical and experimental evidence, however, supports only a minor role for iron contributions to a440 in UGLS lakes. Although both DOC and Fediss were significant variables in linear and log-log regressions on a440, DOC was the stronger predictor; adding Fediss to the linear a440-DOC model improved the R2 only from 0.90 to 0.93. Furthermore, experimental additions of FeIII to colored lake waters had only small effects on a440 (average increase of 0.242 m-1 per 100 μg/L of added FeIII). For 136 visibly stained waters (with a440 > 3.0 m-1), where allochthonous DOM predominates, DOM accounted for 92.3 ± 5.0% of the measured a440 values, and Fediss accounted for the remainder. In 75% of the lakes, Fediss accounted for < 10% of a440, but contributions of 15–30% were observed for 7 river-influenced lakes. Contributions of Fediss in UGLS lakes to specific UV absorbance at 254 nm (SUVA254) generally were also low. Although Fediss accounted for 5–10% of measured SUVA254 in a few samples, on average, 98.1% of the SUVA254 signal was attributable to DOM and only 1.9% to Fediss. DOC predictions from measured a440 were nearly identical to those from a440 corrected to remove Fediss contributions. Overall, variations in Fediss in most UGLS lakes have very small effects on CDOM optical properties, such as a440 and SUVA254, and negligible effects on the accuracy of DOC estimated from a440, data for which can be obtained at broad regional scales by remote sensing methods.

<![CDATA[Conformational regulation of Escherichia coli DNA polymerase V by RecA and ATP]]>

Mutagenic translesion DNA polymerase V (UmuD′2C) is induced as part of the DNA damage-induced SOS response in Escherichia coli, and is subjected to multiple levels of regulation. The UmuC subunit is sequestered on the cell membrane (spatial regulation) and enters the cytosol after forming a UmuD′2C complex, ~ 45 min post-SOS induction (temporal regulation). However, DNA binding and synthesis cannot occur until pol V interacts with a RecA nucleoprotein filament (RecA*) and ATP to form a mutasome complex, pol V Mut = UmuD′2C-RecA-ATP. The location of RecA relative to UmuC determines whether pol V Mut is catalytically on or off (conformational regulation). Here, we present three interrelated experiments to address the biochemical basis of conformational regulation. We first investigate dynamic deactivation during DNA synthesis and static deactivation in the absence of DNA synthesis. Single-molecule (sm) TIRF-FRET microscopy is then used to explore multiple aspects of pol V Mut dynamics. Binding of ATP/ATPγS triggers a conformational switch that reorients RecA relative to UmuC to activate pol V Mut. This process is required for polymerase-DNA binding and synthesis. Both dynamic and static deactivation processes are governed by temperature and time, in which onoff switching is “rapid” at 37°C (~ 1 to 1.5 h), “slow” at 30°C (~ 3 to 4 h) and does not require ATP hydrolysis. Pol V Mut retains RecA in activated and deactivated states, but binding to primer-template (p/t) DNA occurs only when activated. Studies are performed with two forms of the polymerase, pol V Mut-RecA wt, and the constitutively induced and hypermutagenic pol V Mut-RecA E38K/ΔC17. We discuss conformational regulation of pol V Mut, determined from biochemical analysis in vitro, in relation to the properties of pol V Mut in RecA wild-type and SOS constitutive genetic backgrounds in vivo.