Establishing proof of concept for utility of Trueprep®-extracted DNA in line-probe assay testing.

BACKGROUND AND OBJECTIVES: With an increased demand for rapid, diagnostic tools for TB and drug resistance detection, Truenat® MTB-RIF assay has proven to be a rapid point of care molecular test. The present study aimed to establish a proof of concept of using Trueprep-extracted DNA for line-probe assay (LPA) testing.METHODS: A total of 150 sputum samples (MTB-positive at Truenat sites) were divided into two aliquots. One aliquot was used for DNA extraction using the Trueprep device and MTB testing. The second aliquot of the sample was subjected to GenoLyse® DNA extraction. DNA from both the Trueprep and GenoLyse methods was subjected to first-line (FL) and second-line (SL) LPA testing.RESULTS: Of 139 Trueprep-extracted DNA, respectively 135 (97%) and 105 (75%) had interpretable results by FL and SL-LPA testing. Of 128 GenoLyse-extracted DNA, all 128 (100%) had interpretable FL-LPA results and 114 (89%) had interpretable SL-LPA results.CONCLUSION: The results obtained in this study indicate that Trueprep-extracted DNA can be used in obtaining valid LPA results. However, the study needs to be conducted on a larger sample size before our recommendations can be used for policy-making decisions.

Selective Electroporation of Tumor Cells Under AC Radiofrequency Stimulation - A Numerical Study.

Self-consistent evaluations of membrane electroporation along with local heating in single spherical cells arising from external AC radiofrequency electrical stimulation have been carried out. The present numerical study seeks to determine whether healthy and malignant cells exhibit separate electroporative responses with regards to operating frequency. It is shown that cells of Burkitt's lymphoma would respond to frequencies >4.5 MHz, while normal B-cells would have negligible porative effects in that higher frequency range. Similarly, a frequency separation between the response of healthy T-cells and malignant species is predicted with a threshold of about 4 MHz for cancer cells. The present simulation technique is general and so would be able to ascertain the beneficial frequency range for different cell types. The demonstration of higher frequencies to induce poration in malignant cells, while having minimal affecting healthy ones, suggests the possibility of selective electrical targeting for tumor treatments and protocols. It also opens the doorway for tabulating selectivity enhancement regimes as a guide for parameter selection towards more effective treatments while minimizing deleterious effects on healthy cells and tissues.

Importance of surface morphology on secondary electron emission: a case study of Cu covered with carbon, carbon pairs, or graphitic-like layers.

Understanding the relationship between surface adsorbates and secondary electronic emission is critical for a variety of technologies, since the secondary electrons can have deleterious effects on the operation of devices. The mitigation of such phenomena is desirable. Here, using the collective efforts of first-principles, molecular dynamics, and Monte Carlo simulations, we studied the effects of a variety of carbon adsorbates on the secondary electron emission of Cu (110). It was demonstrated that the adsorption of atomic C and C[Formula: see text] pair layers can both reduce and increase the number of secondary electrons depending on the adsorbate coverage. It was shown that under electron irradiation, the C-Cu bonds can be dissociated and reformed into C[Formula: see text] pairs and graphitic-like layers, in agreement with experimental observation. It was verified that the lowest secondary electron emission was due to the formation of the graphitic-like layer. To understand the physical reason for changes in number of secondary electrons for different systems from an electronic structure perspective, two-dimensional potential energy surfaces and charge density contour plots were calculated and analyzed. It was shown that the changes are strongly influenced by the Cu surface morphology and depends highly on the nature of the interactions between the surface Cu and C atoms.

Carbon-oxygen surface formation enhances secondary electron yield in Cu, Ag and Au.

First-principles calculations coupled with Monte Carlo simulations are used to probe the role of a surface CO monolayer formation on secondary electron emission (SEE) from Cu, Ag, and Au (110) materials. It is shown that formation of such a layer increases the secondary electron emission in all systems. Analysis of calculated total density of states (TDOS) in Cu, Ag, and Au, and partial density of states (PDOS) of C and O confirm the formation of a covalent type bonding between C and O atoms. It is shown that such a bond modifies the TDOS and extended it to lower energies, which is then responsible for an increase in the probability density of secondary electron generation. Furthermore, a reduction in inelastic mean free path is predicted for all systems. Our predicted results for the secondary electron yield (SEY) compare very favorably with experimental data in all three materials, and exhibit increases in SEY. This is seen to occur despite increases in the work function for Cu, Ag, and Au. The present analysis can be extended to other absorbates and gas atoms at the surface, and such analyses will be present elsewhere.

Continuum analysis to assess field enhancements for tailoring electroporation driven by monopolar or bipolar pulsing based on nonuniformly distributed nanoparticles.

Recent reports indicate that nanoparticle (NP) clusters near cell membranes could enhance local electric fields, leading to heightened electroporation. This aspect is quantitatively analyzed through numerical simulations whereby time dependent transmembrane potentials are first obtained on the basis of a distributed circuit mode, and the results then used to calculate pore distributions from continuum Smoluchowski theory. For completeness, both monopolar and bipolar nanosecond-range pulse responses are presented and discussed. Our results show strong increases in TMP with the presence of multiple NP clusters and demonstrate that enhanced poration could be possible even over sites far away from the poles at the short pulsing regime. Furthermore, our results demonstrate that nonuniform distributions would work to enable poration at regions far away from the poles. The NP clusters could thus act as distributed electrodes. Our results were roughly in line with recent experimental observations.

Mandating audio-video recording of informed consent: are we right in enforcing this?

Medicines are the result of experimentation carried out in animals and humans. However, there are numerous instances in the history of medicine where humans were subjected to undue risks and abuses, requiring regulations for their safety. Idea of informed consent has found its presence in medical literature from the times of Hippocratic Oath propagating principles of '...never do harm to anyone' and physician directed care of patients. This was revived in post-world war II era in the form of Nuremberg code and the declaration of Helsinki in response to various debilitating experimentations done on prisoners in concentration camps and elsewhere. Complete information and voluntary participation forms the ethical tenets of these acts and the same has been reflected in various guidelines enacted worldwide, which are sufficient to make sure that patient consent is obtained in fair and just manner. Despite this, there have been undesirable lapses in the conduct of clinical trials. This situation worsens, when intentional lapses in conduct of trial hamper the ability of socially and economically disadvantaged communities in developing countries to make free and informed decision.

Evaluations of a mechanistic hypothesis for the influence of extracellular ions on electroporation due to high-intensity, nanosecond pulsing.

The effect of ions present in the extracellular medium on electroporation by high-intensity, short-duration pulsing is studied through molecular dynamic simulations. Our simulation results indicate that mobile ions in the medium might play a role in creating stronger local electric fields across membranes that then reinforce and strengthen electroporation. Much faster pore formation is predicted in higher conductivity media. However, the impact of extracellular conductivity on cellular inflows, which depend on transport processes such as electrophoresis, could be different as discussed here. Our simulation results also show that interactions between cations (Na(+) in this case) and the carbonyl oxygen of the lipid headgroups could impede pore resealing.

Synergistic effects of local temperature enhancements on cellular responses in the context of high-intensity, ultrashort electric pulses.

Results of self-consistent analyses of cells show the possibility of temperature increases at membranes in response to a single nanosecond, high-voltage pulse, at least over small sections of the membrane. Molecular Dynamics simulations indicate that such a temperature increase could facilitate poration, which is one example of a bio-process at the plasma membrane. Our study thus suggests that the use of repetitive high-intensity voltage pulses could open up possibilities for a host of synergistic bio-responses involving both thermal and electrically driven phenomena.

Bioelectric effects of intense ultrashort pulses.

Models for electric field interactions with biological cells predict that pulses with durations shorter than the charging time of the outer membrane can affect intracellular structures. Experimental studies in which human cells were exposed to pulsed electric fields of up to 300 kV/cm amplitude, with durations as short as 10 ns, have confirmed this hypothesis. The observed effects include the breaching of intracellular granule membranes without permanent damage to the cell membrane, abrupt rises in intracellular free calcium levels, enhanced expression of genes, cytochrome c release, and electroporation for gene transfer and drug delivery. At increased electric fields, the application of nanosecond pulses induces apoptosis (programmed cell death) in biological cells, an effect that has been shown to reduce the growth of tumors. Possible applications of the intracellular electroeffects are enhancing gene delivery to the nucleus, controlling cell functions that depend on calcium release (causing cell immobilization), and treating tumors. Such nanosecond electrical pulses have been shown to successfully treat melanoma tumors by using needle arrays as pulse delivery systems. Reducing the pulse duration of intense electric field pulses even further into the subnanosecond range will allow for the use of wideband antennas to deliver the electromagnetic fields into tissue with a spatial resolution in the centimeter range. This review carefully examines the above concepts, provides a theoretical basis, and modeling results based on both continuum approaches and atomistic molecular dynamics methods. Relevant experimental data are also presented, and some of the many potential bioengineering applications discussed.

Transmembrane voltage analyses in spheroidal cells in response to an intense ultrashort electrical pulse.

Self-consistent evaluations of both the transmembrane potential (TMP) and possible electroporation density across membrane of spheroidal cells in response to ultrashort, high-intensity pulses are reported and discussed. Most treatments in the literature have been based on spherical cells, and this represents a step towards more realistic analyses. The present study couples the Laplace equation with Smoluchowski theory of pore formation, to yield dynamic membrane conductivities that influence the TMP. It is shown that the TMP induced by pulsed external voltages can be substantial higher in oblate spheroids as compared to spherical or prolate spheroidal cells. Flattening of the surface area in oblate spheroids leads to both higher electric fields seen by the membrane, and allows a great fraction of the surface area to be porated. This suggests that biomedical applications such as drug delivery and electrochemotherapy could work best for flatter-shaped cells, and secondary field-enabled orienting would be beneficial. Results for arbitrary field orientations and different cell sizes have also been presented.

Self-consistent analyses for potential conduction block in nerves by an ultrashort high-intensity electric pulse.

Simulation studies are presented that probe the possibility of using high-field (> 100 kV/cm) , short-duration ( approximately 50 ns) electrical pulses for nonthermal and reversible cessation of biological electrical signaling pathways. This would have obvious applications in neurophysiology, clinical research, neuromuscular stimulation therapies, and even nonlethal bioweapons development. The concept is based on the creation of a sufficiently high density of pores on the nerve membrane by an electric pulse. This modulates membrane conductance and presents an effective "electrical short" to an incident voltage wave traveling across a nerve. Net blocking of action potential propagation can then result. A continuum approach based on the Smoluchowski equation is used to treat electroporation. This is self-consistently coupled with a distributed circuit representation of the nerve dynamics. Our results indicate that poration at a single neural segment would be sufficient to produce an observable, yet reversible, effect.

Simulations of intracellular calcium release dynamics in response to a high-intensity, ultrashort electric pulse.

Numerical simulations for electrically induced, intracellular calcium release from the endoplasmic reticulum are reported. A two-step model is used for self-consistency. Distributed electrical circuit representation coupled with the Smoluchowski equation yields the ER membrane nanoporation for calcium outflow based on a numerical simulation. This is combined with the continuum Li-Rinzel model and drift diffusion for calcium dynamics. Our results are shown to be in agreement with reported calcium release data. A modest increase (rough doubling) of the cellular calcium is predicted in the absence of extra-cellular calcium. In particular, the applied field of 15 kV/cm with 60 ns pulse duration makes for a strong comparison. No oscillations are predicted and the net recovery period of about 5 min are both in agreement with published experimental results. A quantitative explanation for the lack of such oscillatory behavior, based on the density dependent calcium fluxes, is also provided.

High electrical field effects on cell membranes.

Electrical charging of lipid membranes causes electroporation with sharp membrane conductance increases. Several recent observations, especially at very high field strength, are not compatible with the simple electroporation picture. Here we present several relevant experiments on cell electrical responses to very high external voltages. We hypothesize that, not only are aqueous pores created within the lipid membranes, but that nanoscale membrane fragmentation occurs, possibly with micelle formation. This effect would produce conductivity increases beyond simple electroporation and display a relatively fast turn-off with external voltage. In addition, material loss can be expected at the anode side of cells, in agreement with published experimental reports at high fields. Our hypothesis is qualitatively supported by molecular dynamics simulations. Finally, such cellular responses might temporarily inactivate voltage-gated and ion-pump activity, while not necessarily causing cell death. This hypothesis also supports observations on electrofusion.

Microscopic calculations of local lipid membrane permittivities and diffusion coefficients for application to electroporation analyses.

Interaction of electric fields with biological systems has begun to receive considerable attention for applications that include field-assisted drug delivery, medical interventions, and genetic engineering. External fields induce the strongest effects at membranes with electroporation being a common feature. Membrane transport in this context of poration is often based on continuum approaches utilizing macroscopic parameters such as the permittivity, diffusion coefficients, and mobilities. In such modeling, field dependences, local inhomogeneities, and microscopic details are usually ignored. Here, a molecular dynamics (MD) scheme is used for a more rigorous and physically realistic evaluation of such parameters for potential application to electroporative transport model development. A suitable membrane structure containing a nanopore derived from MD analysis is used as the initial geometric configuration. Both static and frequency dependent diffusion coefficients have been evaluated. Permittivities are also calculated and shown to be dramatically non-uniform in the vicinity of membranes under high external fields. A positive feedback mechanism leading to enhanced membrane fields is discussed.

Plasma membrane voltage changes during nanosecond pulsed electric field exposure.

The change in the membrane potential of Jurkat cells in response to nanosecond pulsed electric fields was studied for pulses with a duration of 60 ns and maximum field strengths of approximately 100 kV/cm (100 V/cell diameter). Membranes of Jurkat cells were stained with a fast voltage-sensitive dye, ANNINE-6, which has a subnanosecond voltage response time. A temporal resolution of 5 ns was achieved by the excitation of this dye with a tunable laser pulse. The laser pulse was synchronized with the applied electric field to record images at times before, during, and after exposure. When exposing the Jurkat cells to a pulse, the voltage across the membrane at the anodic pole of the cell reached values of 1.6 V after 15 ns, almost twice the voltage level generally required for electroporation. Voltages across the membrane on the side facing the cathode reached values of only 0.6 V in the same time period, indicating a strong asymmetry in conduction mechanisms in the membranes of the two opposite cell hemispheres. This small voltage drop of 0.6-1.6 V across the plasma membrane demonstrates that nearly the entire imposed electric field of 10 V/mum penetrates into the interior of the cell and every organelle.

Simulations of nanopore formation and phosphatidylserine externalization in lipid membranes subjected to a high-intensity, ultrashort electric pulse.

A combined MD simulator and time dependent Laplace solver are used to analyze the electrically driven phosphatidylserine externalization process in cells. Time dependent details of nanopore formation at cell membranes in response to a high-intensity (100 kV/cm), ultrashort (10 ns) electric pulse are also probed. Our results show that nanosized pores could typically be formed within about 5 ns. These predictions are in very good agreement with recent experimental data. It is also demonstrated that defect formation and PS externalization in membranes should begin on the anode side. Finally, the simulations confirm that PS externalization is a nanopore facilitated event, rather than the result of molecular translocation across the trans-membrane energy barrier.

Simulations of transient membrane behavior in cells subjected to a high-intensity ultrashort electric pulse.

A molecular dynamics (MD) scheme is combined with a distributed circuit model for a self-consistent analysis of the transient membrane response for cells subjected to an ultrashort (nanosecond) high-intensity (approximately 0.01-V/nm spatially averaged field) voltage pulse. The dynamical, stochastic, many-body aspects are treated at the molecular level by resorting to a course-grained representation of the membrane lipid molecules. Coupling the Smoluchowski equation to the distributed electrical model for current flow provides the time-dependent transmembrane fields for the MD simulations. A good match between the simulation results and available experimental data is obtained. Predictions include pore formation times of about 5-6 ns. It is also shown that the pore formation process would tend to begin from the anodic side of an electrically stressed membrane. Furthermore, the present simulations demonstrate that ions could facilitate pore formation. This could be of practical importance and have direct relevance to the recent observations of calcium release from the endoplasmic reticulum in cells subjected to such ultrashort, high-intensity pulses.

Energy-landscape-model analysis for irreversibility and its pulse-width dependence in cells subjected to a high-intensity ultrashort electric pulse.

We provide a simple, but physical analysis for cell irreversibility and apoptosis in response to an ultrashort (nanosecond), high-intensity electric pulse. Our approach is based on an energy landscape model for determining the temporal evolution of the configurational probability function p(q). The primary focus is on obtaining qualitative predictions of a pulse width dependence to apoptotic cell irreversibility that has been observed experimentally. The analysis couples a distributed electrical model for current flow with the Smoluchowski equation to provide self-consistent, time-dependent transmembrane voltages. The model captures the essence of the experimentally observed pulse-width dependence, and provides a possible physical picture that depends only on the electrical trigger. A number of interesting features are predicted.

Improved energy model for membrane electroporation in biological cells subjected to electrical pulses.

A self-consistent model analysis of electroporation in biological cells has been carried out based on an improved energy model. The simple energy model used in the literature is somewhat incorrect and unphysical for a variety of reasons. Our model for the pore formation energy E(r) includes a dependence on pore population and density. It also allows for variable surface tension, incorporates the effects of finite conductivity on the electrostatic correction term, and is dynamic in nature. Self-consistent calculations, based on a coupled scheme involving the Smoluchowski equation and the improved energy model, are presented. It is shown that E(r) becomes self-adjusting with variations in its magnitude and profile, in response to pore population, and inhibits uncontrolled pore growth and expansion. This theory can be augmented to include pore-pore interactions to move beyond the independent pore picture.