Engineering a serum-resistant and thermostable vesicular stomatitis virus G glycoprotein for pseudotyping retroviral and lentiviral vectors.

Vesicular stomatitis virus G glycoprotein (VSV-G) is the most widely used envelope protein for retroviral and lentiviral vector pseudotyping; however, serum inactivation of VSV-G pseudotyped vectors is a significant challenge for in vivo gene delivery. To address this problem, we conducted directed evolution of VSV-G to increase its resistance to human serum neutralization. After six selection cycles, numerous common mutations were present. On the basis of their location within VSV-G, we analyzed whether substitutions in several surface exposed residues could endow viral vectors with higher resistance to serum. S162T, T230N and T368A mutations enhanced serum resistance, and additionally K66T, T368A and E380K substitutions increased the thermostability of VSV-G pseudotyped retroviral vectors, an advantageous byproduct of the selection strategy. Analysis of a number of combined mutants revealed that VSV-G harboring T230N+T368A or K66T+S162T+T230N+T368A mutations exhibited both higher in vitro resistance to human serum and higher thermostability, as well as enhanced resistance to rabbit and mouse serum. Finally, lentiviral vectors pseudotyped with these variants were more resistant to human serum in a murine model. These serum-resistant and thermostable VSV-G variants may aid the application of retroviral and lentiviral vectors to gene therapy

The possibility of measuring intrinsic electronic correlations in graphene using a d-wave contact Josephson junction

While not widely recognized, electronic correlations might play an important role in graphene. Indeed, Pauling's resonance valence bond (RVB) theory for the pp-bonded planar organic molecules, of which graphene is the infinite extension, already established the importance of the nearest neighbor spin-singlet bond (SB) state in these materials. However, despite the recent growth of interest in graphene, there is still no quantitative estimate of the effects of Coulomb repulsion in either undoped or doped graphene. Here we use a tight-binding Bogoliubov-de Gennes (TB BdG) formalism to show that in unconventional d-wave contact graphene Josephson junctions the intrinsic SB correlations are strongly enhanced. We show on a striking effect of the SB correlations in both proximity effect and Josephson current as well as establishing a 1/(T-T_c) functional dependence for the superconducting decay length. Here T_c is the superconducting transition temperature for the intrinsic SB correlations, which depends on both the effects of Coulomb repulsion and the doping level. We therefore propose that d-wave contact graphene Josephson junctions will provide a promising experimental system for the measurement of the effective strength of intrinsic SB correlations in graphene.Comment: 4 pages, 4 figure

The effect of nearest neighbor spin-singlet correlations in conventional graphene SNS Josephson junctions

Using the self-consistent tight-binding Bogoliubov-de Gennes formalism we have studied the effect of nearest neighbor spin-singlet bond (SB) correlations on Josephson coupling and proximity effect in graphene SNS Josephson junctions with conventional s-wave superconducting contacts. Despite the s-wave superconducting state in the contacts, the SB pairing state inside the junction has d-wave symmetry and clean, sharp interface junctions resemble a 'bulk-meets-bulk' situation with very little interaction between the two different superconducting states. In fact, due to a finite-size suppression of the superconducting state, a stronger SB coupling constant than in the bulk is needed in order to achieve SB pairing in a junction. For both short clean zigzag and armchair junctions a d-wave state that has a zero Josephson coupling to the s-wave state is chosen and therefore the Josephson current decreases when a SB pairing state develops in these junctions. In more realistic junctions, with smoother doping profiles and atomic scale disorder at the interfaces, it is possible to achieve some coupling between the contact s-wave state and the SB d-wave states. In addition, by breaking the appropriate lattice symmetry at the interface in order to induce another d-wave state, a non-zero Josephson coupling can be achieved which leads to a substantial increase in the Josephson current. We also report on the LDOS of the junctions and on a lack of zero energy states at interfaces despite the unconventional order parameters, which we attribute to the near degeneracy of the two d-wave solutions and their mixing at a general interface.Comment: 13 pages, 9 figures. Typos correcte

Modeling soil water dynamics considering measurement uncertainty

In shallow water table controlled environments, surface water management impacts groundwater table levels and soil water dynamics. The study goal was to simulate soil water dynamics in response to canal stage raises considering uncertainty in measured soil water content. WAVE (Water and Agrochemicals in the soil, crop and Vadose Environment) was applied to simulate unsaturated flow above a shallow aquifer. Global sensitivity analysis was performed to identify model input factors with greatest influence on predicted soil water content. Nash-Sutcliffe increased and Root Mean Square Error reduced when uncertainties in measured data were considered in goodness-of-fit calculations using measurement probability distributions and probable asymmetric error boundaries; implying that appropriate model performance evaluation should be done using uncertainty ranges instead of single values. Although uncertainty in the experimental measured data limited evaluation of the absolute predictions by the model, WAVE was found a useful exploratory tool for estimating temporal variation in soil water content. Visual analysis of soil water content time series under proposed changes in canal stage management indicated that sites with land surface elevation of less than 2.0 m NGVD29 were predicted to periodically experience saturated conditions in the root zone and shortening of the growing season if canal stage is raised more than 9 cm and maintained at this level. The models developed could be combined with high resolution digital elevation models in future studies to identify areas with the greatest risk of experiencing saturated root zone. The study also highlighted the need to incorporate measurement uncertainty when evaluating performance of unsaturated flow models

Dynamic factor analysis of surface water management impacts on soil and bedrock water contents in Southern Florida Lowlands

As part of the C111 spreader canal project, structural and operational modifications involving incremental raises in canal stage are planned along one of the major canals (i.e., C111) separating Everglades National Park and agricultural production areas to the east of the park. This study used Dynamic Factor Analysis (DFA) as an alternative tool to physically based models to explore the relationship between different hydrologic variables and the effect of proposed changes in surface water management on soil and bedrock water contents in south Florida. To achieve the goal, objectives were to: (1) use DFA to identify the most important factors affecting temporal variation in soil and bedrock water contents, (2) develop a simplified DFA based regression model for predicting soil and bedrock water contents as a function of canal stage and (3) assess the effect of the proposed incremental raises in canal stage on soil and bedrock water contents. DFA revealed that 5 common trends were the minimum required to describe unexplained variation in the 11 time series studied. Introducing canal stage, water table evaporation and net recharge resulted in lower Akaike information criterion (AIC) and higher Nash-Sutcliffe (C[subscript eff]) values. Results indicated that canal stage significantly (t > 2) drives temporal variation in soil and bedrock water contents, which was represented as scaled frequency while net surface recharge was significant in 7 out of the 11 time series analyzed. The effect of water table evaporation was not significant at all sites. Results also indicated that the most important factor influencing temporal variation in soil and bedrock water contents in terms of regression coefficient magnitude was canal stage. Based on DFA results, a simple regression model was developed to predict soil and bedrock water contents at various elevations as a function of canal stage and net recharge. The performance of the simple model ranged from good (C[subscript eff] ranging from 0.56 to 0.74) to poor (C[subscript eff] ranging from 0.10 to 0.15), performance was better at sites with smaller depths to water table (< 1 m) highlighting the effect of micro-topography on soil and bedrock water content dynamics. Assessment of the effect of 6, 9 and 12 cm increases in canal stage using the simple regression model indicated that changes in temporal variation in soil and bedrock water contents were negligible (average<1.0% average change) at 500 to 2000 m from C111 (or low elevations) which may be attributed to the near saturation conditions already occurring at these sites. This study used DFA to explore the relationship between soil and bedrock water dynamics and surface water stage in shallow water table environments. This approach can be applied to any system in which detailed physical modeling would be limited by inadequate information on parameters or processes governing the physical system

The cell line A-to-I RNA editing catalogue

Adenosine-to-inosine (A-to-I) RNA editing is a common post transcriptional modification. It has a critical role in protecting against false activation of innate immunity by endogenous double stranded RNAs and has been associated with various regulatory processes and diseases such as autoimmune and cardiovascular diseases as well as cancer. In addition, the endogenous A-to-I editing machinery has been recently harnessed for RNA engineering. The study of RNA editing in humans relies heavily on the usage of cell lines as an important and commonly-used research tool. In particular, manipulations of the editing enzymes and their targets are often developed using cell line platforms. However, RNA editing in cell lines behaves very differently than in normal and diseased tissues, and most cell lines exhibit low editing levels, requiring over-expression of the enzymes. Here, we explore the A-to-I RNA editing landscape across over 1000 human cell lines types and show that for almost every editing target of interest a suitable cell line that mimics normal tissue condition may be found. We provide CLAIRE, a searchable catalogue of RNA editing levels across cell lines available at http://srv00.recas.ba.infn.it/atlas/claire.html, to facilitate rational choice of appropriate cell lines for future work on A-to-I RNA editing

Simulating water table response to proposed changes in surface water management in the C-111 agricultural basin of south Florida

As part of an effort to restore the hydrology of Everglades National Park (ENP), incremental raises in canal stage are proposed along a major canal draining south Florida called C-111, which separates ENP from agricultural lands. The study purpose was to use monitoring and modeling to investigate the effect of the proposed incremental raises in canal stage on water table elevation in agricultural lands. The objectives were to: (1) develop a MODFLOW based model for simulating groundwater flow within the study area, (2) apply the developed model to determine if the proposed changes in canal stage result in significant changes in water table elevation, root zone saturation or groundwater flooding and (3) assess aquifer response to large rainfall events. Results indicate the developed model was able to reproduce measured water table elevation with an average Nash-Sutcliffe > 0.9 and Root Mean Square Error 2 year return period storm), reduced water table intrusion into the root zone. We conclude that the impact of operational changes in canal stage management on root zone saturation and groundwater flooding depended on micro-topography within the field and depth of storm events. The findings of this study can be used in fine tuning canal stage operations to minimize root zone saturation and groundwater flooding of agricultural fields while maximizing environmental benefits through increased water flow in the natural wetland areas. This study also highlights the benefit of detailed field scale simulations

The structure of the COPI coat determined within the cell

COPI-coated vesicles mediate trafficking within the Golgi apparatus and from the Golgi to the endoplasmic reticulum. The structures of membrane protein coats, including COPI, have been extensively studied with in vitro reconstitution systems using purified components. Previously we have determined a complete structural model of the in vitro reconstituted COPI coat (Dodonova et al., 2017). Here, we applied cryo-focused ion beam milling, cryo-electron tomography and subtomogram averaging to determine the native structure of the COPI coat within vitrified Chlamydomonas reinhardtii cells. The native algal structure resembles the in vitro mammalian structure, but additionally reveals cargo bound beneath β’–COP. We find that all coat components disassemble simultaneously and relatively rapidly after budding. Structural analysis in situ, maintaining Golgi topology, shows that vesicles change their size, membrane thickness, and cargo content as they progress from cis to trans, but the structure of the coat machinery remains constant

Photogeneration Dynamics of a Soliton Pair in Polyacetylene

Dynamical process of the formation of a soliton pair from a photogenerated electron-hole pair in polyacetylene is studied numerically by adopting the SSH Hamiltonian. A weak local disorder is introduced in order to trigger the formation. Starting from an initial configuration with an electron at the bottom of the conduction band and a hole at the top of the valence band, separated by the Peierls gap, the time dependent Schr${\rm \ddot{o}}$ndinger equation for the electron wave functions and the equation of motion for the lattice displacements are solved numerically. After several uniform oscillations of the lattice system at the early stage, a large distortion corresponding to a pair of a soliton and an anti-soliton develops from a point which is determined by the location and type of the disorder. In some cases, two solitons run in opposite directions, leaving breather like oscillations behind, and in other cases they form a bound state emitting acoustic lattice vibrational modes.Comment: 16 pages 7 figure