Transient protonic capacitor: Explaining the bacteriorhodopsin membrane experiment of Heberle et al. 1994.

The transmembrane-electrostatically localized protons (TELP) theory can serve as a unified framework to explain experimental observations and elucidate bioenergetic systems including both delocalized and localized protonic coupling. With the TELP model as a unified framework, it is now better explained how the bacteriorhodopsin-purple membrane-ATPase system functions. The bacteriorhodopsin pumping of protons across the membrane results in the formation of TELP around the halobacterial extracellular membrane surface that is perfectly positioned to drive ATP synthase for the synthesis of ATP from ADP and Pi. The bacteriorhodopsin purple membrane sheet experiment of Heberle et al. 1994 is now better explained here as a transient "protonic capacitor". During the lifetime of a flashlight-induced protonic bacteriorhodopsin purple membrane capacitor activity, there is at least a transient non-zero membrane potential (Δψ ≠ 0). The experimental results demonstrated that "after proton release by an integral membrane protein, long-range proton transfer along the membrane surface is faster than proton exchange with the bulk water phase" exactly as predicted by the TELP theory, which is fundamentally important to the science of bioenergetics.

Protonic conductor: Explaining the transient "excess protons" experiment of Pohl's group 2012.

The transmembrane-electrostatically localized protons (TELP) theory can serve as a unified framework to explain experimental observations and elucidate bioenergetic systems including both delocalized and localized protonic coupling. With the TELP model as a unified framework, we can now better explain: the experimental results of Pohl's group (Zhang et al. 2012) as an effect of transient "excess protons" that can temporally form because of the difference between the fast protonic conduction in liquid water through the "hops and turns" mechanism and the relatively slow diffusion of chloride anions. This new understanding with the TELP theory agrees well with the independent analysis on the Pohl's lab group experiment results by Agmon and Gutman who also concluded that "the excess protons propagate as an advancing front".

Ozonized biochar filtrate effects on the growth of Pseudomonas putida and cyanobacteria Synechococcus elongatus PCC 7942.

BACKGROUND: Biochar ozonization was previously shown to dramatically increase its cation exchange capacity, thus improving its nutrient retention capacity. The potential soil application of ozonized biochar warrants the need for a toxicity study that investigates its effects on microorganisms. RESULTS: In the study presented here, we found that the filtrates collected from ozonized pine 400 biochar and ozonized rogue biochar did not have any inhibitory effects on the soil environmental bacteria Pseudomonas putida, even at high dissolved organic carbon (DOC) concentrations of 300 ppm. However, the growth of Synechococcus elongatus PCC 7942 was inhibited by the ozonized biochar filtrates at DOC concentrations greater than 75 ppm. Further tests showed the presence of some potential inhibitory compounds (terephthalic acid and p-toluic acid) in the filtrate of non-ozonized pine 400 biochar; these compounds were greatly reduced upon wet-ozonization of the biochar material. Nutrient detection tests also showed that dry-ozonization of rogue biochar enhanced the availability of nitrate and phosphate in its filtrate, a property that may be desirable for soil application. CONCLUSION: Ozonized biochar substances can support soil environmental bacterium Pseudomonas putida growth, since ozonization detoxifies the potential inhibitory aromatic molecules.

Mitochondrial energetics with transmembrane electrostatically localized protons: do we have a thermotrophic feature?

Transmembrane electrostatically localized protons (TELP) theory has been recently recognized as an important addition over the classic Mitchell's chemiosmosis; thus, the proton motive force (pmf) is largely contributed from TELP near the membrane. As an extension to this theory, a novel phenomenon of mitochondrial thermotrophic function is now characterized by biophysical analyses of pmf in relation to the TELP concentrations at the liquid-membrane interface. This leads to the conclusion that the oxidative phosphorylation also utilizes environmental heat energy associated with the thermal kinetic energy (kBT) of TELP in mitochondria. The local pmf is now calculated to be in a range from 300 to 340 mV while the classic pmf (which underestimates the total pmf) is in a range from 60 to 210 mV in relation to a range of membrane potentials from 50 to 200 mV. Depending on TELP concentrations in mitochondria, this thermotrophic function raises pmf significantly by a factor of 2.6 to sixfold over the classic pmf. Therefore, mitochondria are capable of effectively utilizing the environmental heat energy with TELP for the synthesis of ATP, i.e., it can lock heat energy into the chemical form of energy for cellular functions.

Energy Renewal: Isothermal Utilization of Environmental Heat Energy with Asymmetric Structures.

Through the research presented herein, it is quite clear that there are two thermodynamically distinct types (A and B) of energetic processes naturally occurring on Earth. Type A, such as glycolysis and the tricarboxylic acid cycle, apparently follows the second law well; Type B, as exemplified by the thermotrophic function with transmembrane electrostatically localized protons presented here, does not necessarily have to be constrained by the second law, owing to its special asymmetric function. This study now, for the first time, numerically shows that transmembrane electrostatic proton localization (Type-B process) represents a negative entropy event with a local protonic entropy change (ΔSL) in a range from -95 to -110 J/K∙mol. This explains the relationship between both the local protonic entropy change (ΔSL) and the mitochondrial environmental temperature (T) and the local protonic Gibbs free energy (ΔGL=TΔSL) in isothermal environmental heat utilization. The energy efficiency for the utilization of total protonic Gibbs free energy (ΔGT including ΔGL=TΔSL) in driving the synthesis of ATP is estimated to be about 60%, indicating that a significant fraction of the environmental heat energy associated with the thermal motion kinetic energy (kBT) of transmembrane electrostatically localized protons is locked into the chemical form of energy in ATP molecules. Fundamentally, it is the combination of water as a protonic conductor, and thus the formation of protonic membrane capacitor, with asymmetric structures of mitochondrial membrane and cristae that makes this amazing thermotrophic feature possible. The discovery of energy Type-B processes has inspired an invention (WO 2019/136037 A1) for energy renewal through isothermal environmental heat energy utilization with an asymmetric electron-gated function to generate electricity, which has the potential to power electronic devices forever, including mobile phones and laptops. This invention, as an innovative Type-B mimic, may have many possible industrial applications and is likely to be transformative in energy science and technologies for sustainability on Earth.

Protonic conductor: better understanding neural resting and action potential.

With the employment of the transmembrane electrostatic proton localization theory with a new membrane potential equation, neural resting and action potential is now much better understood as the voltage contributed by the localized protons/cations at a neural liquid- membrane interface. Accordingly, the neural resting/action potential is essentially a protonic/cationic membrane capacitor behavior. It is now understood with a newly formulated action potential equation: when action potential is <0 (negative number), the localized protons/cations charge density at the liquid-membrane interface along the periplasmic side is >0 (positive number); when the action potential is >0, the concentration of the localized protons and localized nonproton cations is <0, indicating a "depolarization" state. The nonlinear curve of the localized protons/cations charge density in the real-time domain of an action potential spike appears as an inverse mirror image to the action potential. The newly formulated action potential equation provides biophysical insights for neuron electrophysiology, which may represent a complementary development to the classic Goldman-Hodgkin-Katz equation. With the use of the action potential equation, the biological significance of axon myelination is now also elucidated as to provide protonic insulation and prevent any ions both inside and outside of the neuron from interfering with the action potential signal, so that the action potential can quickly propagate along the axon with minimal (e.g., 40 times less) energy requirement.NEW & NOTEWORTHY The newly formulated action potential equation provides biophysical insights for neuron electrophysiology, which may represent a complementary development to the classic Goldman-Hodgkin-Katz equation. The nonlinear curve of the localized protons/cations charge density in the real-time domain of an action potential spike appears as an inverse mirror image to the action potential. The biological significance of axon myelination is now elucidated as to provide protonic insulation and prevent any ions from interfering with action potential signal.

Isothermal Environmental Heat Energy Utilization by Transmembrane Electrostatically Localized Protons at the Liquid-Membrane Interface.

This study employing the latest theory on transmembrane electrostatic proton localization has now, for the first time, consistently elucidated a decades-longstanding bioenergetic conundrum in alkalophilic bacteria and more importantly discovered an entirely new feature: isothermal environmental heat utilization by electrostatically localized protons at the liquid-membrane interface. It was surprisingly revealed that the protonic motive force (equivalent to Gibbs free energy) from the isothermal environmental heat energy utilization through the electrostatically localized protons is not constrained by the overall energetics of the redox-driven proton pump system because of the following: (a) the transmembrane electrostatically localized protons are not free to move away from the membrane surface as a protonic capacitor feature; (b) the proton pumps embedded in the cell membrane extend beyond the localized proton layer apparently as an asymmetric property of the biological membrane; and (c) the protonic inlet mouth of the ATP synthase that accepts protons is located within this layer as another natural property of the asymmetric biological membrane. This work has now, for the first time, shown a novel thermotrophic feature where biological systems can isothermally utilize environmental heat energy through transmembrane electrostatically localized protons to help drive ATP synthesis.

Protonic Capacitor: Elucidating the biological significance of mitochondrial cristae formation.

For decades, it was not entirely clear why mitochondria develop cristae? The work employing the transmembrane-electrostatic proton localization theory reported here has now provided a clear answer to this fundamental question. Surprisingly, the transmembrane-electrostatically localized proton concentration at a curved mitochondrial crista tip can be significantly higher than that at the relatively flat membrane plane regions where the proton-pumping respiratory supercomplexes are situated. The biological significance for mitochondrial cristae has now, for the first time, been elucidated at a protonic bioenergetics level: 1) The formation of cristae creates more mitochondrial inner membrane surface area and thus more protonic capacitance for transmembrane-electrostatically localized proton energy storage; and 2) The geometric effect of a mitochondrial crista enhances the transmembrane-electrostatically localized proton density to the crista tip where the ATP synthase can readily utilize the localized proton density to drive ATP synthesis.

Electrostatically localized proton bioenergetics: better understanding membrane potential.

In Mitchell's chemiosmotic theory, membrane potential Δ ψ was given as the electric potential difference across the membrane. However, its physical origin for membrane potential Δ ψ was not well explained. Using the Lee proton electrostatic localization model with a newly formulated equation for protonic motive force (pmf) that takes electrostatically localized protons into account, membrane potential has now been better understood as the voltage difference contributed by the localized surface charge density ( [ H L + ] + ∑ i = 1 n [ M L i + ] ) at the liquid-membrane interface as in an electrostatically localized protons/cations-membrane-anions capacitor. That is, the origin of membrane potential Δ ψ is now better understood as the electrostatic formation of the localized surface charge density that is the sum of the electrostatically localized proton concentration [ H L + ] and the localized non-proton cations density ∑ i = 1 n [ M L i + ] at the liquid membrane interface. The total localized surface charge density equals to the ideal localized proton population density [ H L + ] 0 before the cation-proton exchange process; since the cation-proton exchange process does not change the total localized charges density, neither does it change to the membrane potential Δ ψ . The localized proton concentration [ H L + ] represents the dominant component, which accounts about 78% of the total localized surface charge density at the cation-proton exchange equilibrium state in animal mitochondria. Liquid water as a protonic conductor may play a significant role in the biological activities of membrane potential formation and utilization.

Protocol measuring horizontal gene transfer from algae to non-photosynthetic organisms.

Horizontal gene transfer (HGT) is a natural process for an organism to transfer genetic material to another organism that is a completely different species, for example, from a blue-green alga to a non-photosynthetic bacterium. The phenomenon of HGT is not only of an interest to the science of molecular genetics and biology, but also to the biosafety issue of genetic engineering. The novel protocol reported here for the first time teaches how to measure HGT from a genetically engineered (GE) blue-green alga (gene donor) to wild-type E. coli (recipient). This novel protocol can be used to measure HGT frequency for both plasmid transgenes and/or genomic transgenes from a donor to recipient organism. •According to this novel protocol, the HGT frequency may be calculated from the number of HGT recipient colonies observed, the number of recipient cells plated, and the donor-recipient co-incubation time.•This approach can also help test the possible HGT routes to assess whether a HGT is through a direct cell-to-cell interaction or by an indirect cell-to-liquid environment-to-cell process.•The protocol may be applied in full and/or in part with adjustments to measure HGT for a wide range of donor and recipient organisms of interest.