Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proton gradients and pH oscillations emerge from heat flow at the microscale.

ABSTRACT: Proton gradients are essential for biological systems. They not only drive the synthesis of ATP, but initiate molecule degradation and recycling inside lysosomes. However, the high mobility and permeability of protons through membranes make pH gradients very hard to sustain in vitro. Here we report that heat flow across a water-filled chamber forms and sustains stable pH gradients. Charged molecules accumulate by convection and thermophoresis better than uncharged species. In a dissociation reaction, this imbalances the reaction equilibrium and creates a difference in pH. In solutions of amino acids, phosphate, or nucleotides, we achieve pH differences of up to 2?pH units. The same mechanism cycles biomolecules by convection in the created proton gradient. This implements a feedback between biomolecules and a cyclic variation of the pH. The finding provides a mechanism to create a self-sustained proton gradient to drive biochemical reactions.

SUBMITTER: Keil LMR

PROVIDER: S-EPMC5711904 | biostudies-other | 2017 Dec

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Publications

Proton gradients and pH oscillations emerge from heat flow at the microscale.

Keil Lorenz M R LMR Möller Friederike M FM Kieß Michael M Kudella Patrick W PW Mast Christof B CB

Nature communications 20171201 1

Proton gradients are essential for biological systems. They not only drive the synthesis of ATP, but initiate molecule degradation and recycling inside lysosomes. However, the high mobility and permeability of protons through membranes make pH gradients very hard to sustain in vitro. Here we report that heat flow across a water-filled chamber forms and sustains stable pH gradients. Charged molecules accumulate by convection and thermophoresis better than uncharged species. In a dissociation reac ...[more]

PMID: 29196673

Similar Datasets

Microscale gradients of oxygen, hydrogen peroxide, and pH in freshwater cathodic biofilms.

Project description:Cathodic reactions in biofilms employed in sediment microbial fuel cells is generally studied in the bulk phase. However, the cathodic biofilms affected by these reactions exist in microscale conditions in the biofilm and near the electrode surface that differ from the bulk phase. Understanding these microscale conditions and relating them to cathodic biofilm performance is critical for better-performing cathodes. The goal of this research was to quantify the variation in oxygen, hydrogen peroxide, and the pH value near polarized surfaces in river water to simulate cathodic biofilms. We used laboratory river-water biofilms and pure culture biofilms of Leptothrix discophora SP-6 as two types of cathodic biofilms. Microelectrodes were used to quantify oxygen concentration, hydrogen peroxide concentration, and the pH value near the cathodes. We observed the correlation between cathodic current generation, oxygen consumption, and hydrogen peroxide accumulation. We found that the 2 e(-) pathway for oxygen reduction is the dominant pathway as opposed to the previously accepted 4 e(-) pathway quantified from bulk-phase data. Biofouling of initially non-polarized cathodes by oxygen scavengers reduced cathode performance. Continuously polarized cathodes could sustain a higher cathodic current longer despite contamination. The surface pH reached a value of 8.8 when a current of only -30 μA was passed through a polarized cathode, demonstrating that the pH value could also contribute to preventing biofouling. Over time, oxygen-producing cathodic biofilms (Leptothrix discophora SP-6) colonized on polarized cathodes, which decreased the overpotential for oxygen reduction and resulted in a large cathodic current attributed to manganese reduction. However, the cathodic current was not sustainable.

| S-EPMC4247834 | biostudies-literature

Microrheology reveals microscale viscosity gradients in planktonic systems.

Project description:Microbial activity in planktonic systems creates a dynamic and heterogeneous microscale seascape that harbors a diverse community of microorganisms and ecological interactions of global significance. In recent decades great effort has been put into understanding this complex system, particularly focusing on the role of chemical patchiness, while overlooking a physical parameter that governs microbial life and is affected by biological activity: viscosity. Here we reveal spatial heterogeneity of viscosity in planktonic systems by using microrheological techniques that allow measurement of viscosity at length scales relevant to microorganisms. We show the viscous nature and the spatial extent of the phycosphere, the region surrounding phytoplankton. In ∼45% of the phytoplankton cells analyzed we detected increases in viscosity that extended up to 30 µm away from the cell with up to 40 times the viscosity of seawater. We also show how these gradients of viscosity can be amplified around a lysing phytoplankton cell as its viscous contents leak away. Finally, we report conservative estimates of viscosity inside marine aggregates, hotspots of microbial activity, more than an order of magnitude higher than in seawater. Since the diffusivities of dissolved molecules, particles, and microorganisms are inversely related to viscosity, microheterogeneity in viscosity alters the microscale distribution of microorganisms and their resources, with pervasive implications for the functioning of the planktonic ecosystem. Increasing viscosities impacts ecological interactions and processes, such as nutrient uptake, chemotaxis, and particle encounter, that occur at the microscale but influence carbon and nutrient cycles at a global scale.

| S-EPMC7817219 | biostudies-literature

Stretching and folding sustain microscale chemical gradients in porous media.

Project description:Fluid flow in porous media drives the transport, mixing, and reaction of molecules, particles, and microorganisms across a wide spectrum of natural and industrial processes. Current macroscopic models that average pore-scale fluctuations into an effective dispersion coefficient have shown significant limitations in the prediction of many important chemical and biological processes. Yet, it is unclear how three-dimensional flow in porous structures govern the microscale chemical gradients controlling these processes. Here, we obtain high-resolution experimental images of microscale mixing patterns in three-dimensional porous media and uncover an unexpected and general mixing mechanism that strongly enhances concentration gradients at pore-scale. Our experiments reveal that systematic stretching and folding of fluid elements are produced in the pore space by grain contacts, through a mechanism that leads to efficient microscale chaotic mixing. These insights form the basis for a general kinematic model linking chaotic-mixing rates in the fluid phase to the generic structural properties of granular matter. The model successfully predicts the resulting enhancement of pore-scale chemical gradients, which appear to be orders of magnitude larger than predicted by dispersive approaches. These findings offer perspectives for predicting and controlling the vast diversity of reactive transport processes in natural and synthetic porous materials, beyond the current dispersion paradigm.

| S-EPMC7306761 | biostudies-literature

Microscale pH regulation by splitting water.

Project description:We present a simple, flexible approach for pH regulation in micro-chambers by injecting controllable amounts of protons and hydroxide ions via field-enhanced dissociation of water molecules. Under a DC voltage bias, the polymeric bipolar membranes integrated in microfluidics devices generate and separate H(+) and OH(-) ions without gas production or contaminant generation resulting from electron-transfer reactions. Robust local on-chip pH and pH gradients are sustained with no need of additional acidic∕basic solutions that dilute analyte concentrations. The method could provide a better strategy for pH control in microfluidics.

| S-EPMC3223509 | biostudies-other

pH Distribution along Growing Fungal Hyphae at Microscale.

Project description:Creating unique microenvironments, hyphal surfaces and their surroundings allow for spatially distinct microbial interactions and functions at the microscale. Using a microfluidic system and pH-sensitive whole-cell bioreporters (Synechocystis sp. PCC6803) attached to hyphae, we spatially resolved the pH along surfaces of growing hyphae of the basidiomycete Coprinopsis cinerea. Time-lapse microscopy analysis of ratiometric fluorescence signals of >2400 individual bioreporters revealed an overall pH drop from 6.3 ± 0.4 (n = 2441) to 5.0 ± 0.3 (n = 2497) within 7 h after pH bioreporter loading to hyphal surfaces. The pH along hyphal surfaces varied significantly (p < 0.05), with pH at hyphal tips being on average ~0.8 pH units lower than at more mature hyphal parts near the entrance of the microfluidic observation chamber. Our data represent the first dynamic in vitro analysis of surface pH along growing hyphae at the micrometre scale. Such knowledge may improve our understanding of spatial, pH-dependent hyphal processes, such as the degradation of organic matter or mineral weathering.

| S-EPMC9224906 | biostudies-literature

An aquatic microrobot for microscale flow manipulation.

Project description:Microrobots have been developed and extensively employed for performing the variety tasks with various applications. However, the intricate fabrication and actuation processes employed for microrobots further restrict their multitudinous applicability as well as the controllability in high accuracy. As an alternative, in this work an aquatic microrobot was developed using a distinctive concept of the building block technique where the microrobot was built based on the block to block design. An in-house electromagnetic system as well as the control algorithm were developed to achieve the precise real-time dynamics of the microrobot for extensive applications. In addition, pivotal control parameters of the microrobot including the actuating waveforms together with the operational parameters were verified and discussed in conjunction with the magnetic intensity simulation. A mixing task was performed with high efficiency based on the trajectory planning and rotation control of the microrobot to demonstrate its capability in flow manipulation which can be advantageous for microreactor applications down the load. Aside from it, a dissolution test was further conducted to provide an on-demand flow agitation function of the microrobot for the next level of lab chip applications. The presented work with detail dynamic analysis is envisaged to provide a new look of microrobot control and functions from the engineering perspective with profoundly potential applications.

| S-EPMC8942993 | biostudies-literature

Global reef fish richness gradients emerge from divergent and scale-dependent component changes.

Project description:Biodiversity varies from place to place due to environmental and historical factors. To improve our understanding of how history and the environment influence observed patterns, we need to address the limitations of the most commonly used biodiversity metric, species richness. Here, we show that scale-dependent dissections of species richness into components of total abundance, species relative abundances and spatial aggregations of species reveal that two well-known biogeographic reef fish species richness gradients emerge from very different underlying component patterns. Latitudinal richness is underpinned by scale-independent patterns of total and relative abundances, suggesting ecological constraints scale up to determine abundances within communities. In contrast, the longitudinal gradient of species richness typically attributed to historical biogeography only emerges at the largest scale and is accompanied by a similar pattern of relative abundances, suggesting that site-to-site compositional variation leading to species aggregation (i.e. a component of ?-diversity) underlies this gradient. Examining relationships among the components that underpin biodiversity gradients reveals new patterns that can better identify processes influencing patterns of biodiversity.

| S-EPMC5719164 | biostudies-literature

Dynamic air/liquid pockets for guiding microscale flow.

Project description:Microscale flows of fluids are mainly guided either by solid matrices or by liquid-liquid interfaces. However, the solid matrices are plagued with persistent fouling problems, while liquid-liquid interfaces are limited to low-pressure applications. Here we report a dynamic liquid/solid/gas material containing both air and liquid pockets, which are formed by partially infiltrating a porous matrix with a functional liquid. Using detailed theoretical and experimental data, we show that the distribution of the air- and liquid-filled pores is responsive to pressure and enables the formation and instantaneous recovery of stable liquid-liquid interfaces that sustain a wide range of pressures and prevent channel contamination. This adaptive design is demonstrated for polymeric materials and extended to metal-based systems that can achieve unmatched mechanical and thermal stability. Our platform with its unique adaptive pressure and antifouling capabilities may offer potential solutions to flow control in microfluidics, medical devices, microscale synthesis, and biological assays.

| S-EPMC5821814 | biostudies-other

Shear dependent red blood cell adhesion in microscale flow.

Project description:Non-adherence and deformability are the key intrinsic biomechanical features of the red blood cell (RBC), which allow it to tightly squeeze and pass through even the narrowest of microcirculatory networks. Blockage of microcirculatory flow, also known as vaso-occlusion, is a consequence of abnormal cellular adhesion to the vascular endothelium. In sickle cell disease (SCD), an inherited anaemia, even though RBCs have been shown to be heterogeneous in adhesiveness and deformability, this has not been studied in the context of physiologically relevant dynamic shear gradients at the microscale. We developed a microfluidic system that simulates physiologically relevant shear gradients of microcirculatory blood flow at a constant single volumetric flow rate. Using this system, shear dependent adhesion of RBCs from 28 subjects with SCD and from 11 healthy subjects was investigated using vascular endothelial protein functionalized microchannels. We defined a new term, RBC Shear Gradient Microfluidic Adhesion (SiGMA) index to assess shear dependent RBC adhesion in a subject-specific manner. We have shown for the first time that shear dependent adhesion of RBCs is heterogeneous in a microfluidic flow model, which correlates clinically with inflammatory markers and iron overload in subjects with SCD. This study reveals the complex dynamic interactions between RBC-mediated microcirculatory occlusion and clinical outcomes in SCD. These interactions may also be relevant to other microcirculatory disorders and microvascular diseases.

| S-EPMC6421573 | biostudies-literature

Dynamic microscale flow patterning using electrical modulation of zeta potential.

Project description:The ability to move fluids at the microscale is at the core of many scientific and technological advancements. Despite its importance, microscale flow control remains highly limited by the use of discrete channels and mechanical valves, and relies on fixed geometries. Here we present an alternative mechanism that leverages localized field-effect electroosmosis to create dynamic flow patterns, allowing fluid manipulation without the use of physical walls. We control a set of gate electrodes embedded in the floor of a fluidic chamber using an ac voltage in sync with an external electric field, creating nonuniform electroosmotic flow distributions. These give rise to a pressure field that drives the flow throughout the chamber. We demonstrate a range of unique flow patterns that can be achieved, including regions of recirculating flow surrounded by quiescent fluid and volumes of complete stagnation within a moving fluid. We also demonstrate the interaction of multiple gate electrodes with an externally generated flow field, allowing spatial modulation of streamlines in real time. Furthermore, we provide a characterization of the system in terms of time response and dielectric breakdown, as well as engineering guidelines for its robust design and operation. We believe that the ability to create tailored microscale flow using solid-state actuation will open the door to entirely new on-chip functionalities.

| S-EPMC6534970 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data