Biophysics Community Research Articles

N2O Is an Important Piece of the Puzzle, but Seeing the Whole Picture Strengthens Denitrification Research

AbstractFor decades, denitrification research has been limited by the challenge of measuring fluxes of N2 against a background of high atmospheric concentrations. The methods developed to overcome this challenge all have strengths and weaknesses. Weitzman et al. (2021, https://doi.org/10.1029/2020JG006234) demonstrate the potential of one technique, the Nitrogen‐Free Air Recirculation Method, to measure denitrification end‐products in relatively undisturbed soil cores. This work reinforces the importance of N2 as the primary end‐product of denitrification, accounting for over 86% of measured fluxes in all cores sampled, and reveals unforeseen hotspots of denitrification at depth in soil. These findings are consistent with a similar effort to improve estimates of N2O: N2O + N2 yield at the field scale that predicts N2 fluxes two to three times higher than predicted using previous estimates. By providing a more complete picture of N2O and N2 production in terrestrial systems, these efforts can strengthen denitrification research and support essential refinement of ecosystem models. The identification of unforeseen denitrification hotspots highlights the continued surprises of soil nitrogen cycle and should inspire mechanistic research into the biophysical drivers and communities that mediate denitrification hotspots.

Mangrove Biophysical Condition and Community’s Socio-economic Profile as Managers of Mangrove Forest in Tagpait, Aborlan and Bacungan Puerto Princesa City, Palawan, Philippines

The mangrove forest in Tagpait, Aborlan, is being managed by the Indigenous Cultural Community (Tagbanua Tribe) through their organization, the Tagpait Coastal Development Association (TACDA). Bacungan Mangrove Eco-tourism Service Cooperative is managing the Bacungan mangrove forest. The area was engaged in tourism activity until now through paddle boating, floating restaurant, mangrove adventure. This study used the household interview to determine the socio-economic profile and quadrat to assess mangrove biophysical condition. Results show that Bacungan is more diverse, with a higher number of species present in the area with 13 mangrove species while eight in Tagpait. The most dominant mangrove species in Tagpait is Rhizophora apiculata (39%), while Rhizophora mucronata in Bacungan (22%). Most of the respondents in Tagpait are fishers, which about 20%, then 14% are involved in buy and sell of marine products, and 5% are engaged in the processing of marine products. In Bacungan, the majority are engaged in fishing livelihood (37%), 13% are involved in buy and sell of marine products, and 4% are engaged in the processing of marine products.

Beyond Ticking Boxes: Holistic Assessment of Travel Award Programs Is Essential for Inclusivity

Beyond Ticking Boxes: Holistic Assessment of Travel Award Programs Is Essential for Inclusivity

Interaction standards for biophysics: anti-lysozyme nanobodies

There is a significant demand in the molecular biophysics community for robust standard samples. They are required by researchers, instrument developers and pharmaceutical companies for instrumental quality control, methodological development and in the design and validation of devices, diagnostics and instrumentation. To-date there has been no clear consensus on the need and type of standards that should be available and different research groups and instrument manufacturers use different standard systems which significantly hinders comparative analysis. One of the major objectives of the Association of Resources for Biophysical Research in Europe (ARBRE) is to establish a common set of standard samples that can be used throughout the biophysics community and instrument developers. A survey was circulated among ARBRE members to ascertain the requirements of laboratories when using standard systems and the results are documented in this article. In summary, the major requirements are protein samples which are cheap, relatively small, stable and have different binding strengths. We have developed a panel of sdAb’s or ‘nanobodies’ against hen-egg white lysozyme with different binding strengths and suitable stability characteristics. Here we show the results of the survey, the selection procedure, validation and final selection of a panel of nanobody interaction standards.

OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations.

We present OpenAWSEM and Open3SPN2, new cross-compatible implementations of coarse-grained models for protein (AWSEM) and DNA (3SPN2) molecular dynamics simulations within the OpenMM framework. These new implementations retain the chemical accuracy and intrinsic efficiency of the original models while adding GPU acceleration and the ease of forcefield modification provided by OpenMM's Custom Forces software framework. By utilizing GPUs, we achieve around a 30-fold speedup in protein and protein-DNA simulations over the existing LAMMPS-based implementations running on a single CPU core. We showcase the benefits of OpenMM's Custom Forces framework by devising and implementing two new potentials that allow us to address important aspects of protein folding and structure prediction and by testing the ability of the combined OpenAWSEM and Open3SPN2 to model protein-DNA binding. The first potential is used to describe the changes in effective interactions that occur as a protein becomes partially buried in a membrane. We also introduced an interaction to describe proteins with multiple disulfide bonds. Using simple pairwise disulfide bonding terms results in unphysical clustering of cysteine residues, posing a problem when simulating the folding of proteins with many cysteines. We now can computationally reproduce Anfinsen's early Nobel prize winning experiments by using OpenMM's Custom Forces framework to introduce a multi-body disulfide bonding term that prevents unphysical clustering. Our protein-DNA simulations show that the binding landscape is funneled towards structures that are quite similar to those found using experiments. In summary, this paper provides a simulation tool for the molecular biophysics community that is both easy to use and sufficiently efficient to simulate large proteins and large protein-DNA systems that are central to many cellular processes. These codes should facilitate the interplay between molecular simulations and cellular studies, which have been hampered by the large mismatch between the time and length scales accessible to molecular simulations and those relevant to cell biology.

Vague property status and future risk of mangroves: lesson learned from South Sulawesi, Indonesia

Mangrove forest management in South Sulawesi is challenging due to jurisdictional boundaries to biophysical processes, resource characteristics, and community development dynamics. The research aims to study the future risk of mangrove forest management growing on accretion land due to its vague status. Data and information were collected through in-depth interviews involving 17 key-informants selected by using the snowball method. Mangrove forest in the research site grows on accretion land, and it was classified as state property with Common Pool Resources (CPR) characteristics. Late attendance of the Indonesian government has instigated the “de jure” status of accretion land becomes illegitimate as the local community does not recognize it as state property. The situation leads to the ambiguity of mangrove forest property status, resulting in multilayer property formulation for several products/services/benefits generated. Several strategies to prevent its transformation into other usages are proposed, i.e., (a) improve the community understanding of the economic value of mangrove resource and risk if vanished; (b) strengthening and intensive socialization of regulations both at the local and higher-level; and (c) providing legal access for the community to manage mangrove forest through the development of Social Forestry Program in the area.

Engaging with the science and politics of biodiversity futures: a literature review

SummaryFuture global environmental change will have a significant impact on biodiversity through the intersecting forces of climate change, urbanization, human population growth, overexploitation, and pollution. This presents a fundamental challenge to conservation approaches, which seek to conserve past or current assemblages of species or ecosystems in situ. This review canvases diverse approaches to biodiversity futures, including social science scholarship on the Anthropocene and futures thinking alongside models and scenarios from the biophysical science community. It argues that charting biodiversity futures requires processes that must include broad sections of academia and the conservation community to ask what desirable futures look like, and for whom. These efforts confront political and philosophical questions about levels of acceptable loss, and how trade-offs can be made in ways that address the injustices in the distribution of costs and benefits across and within human and non-human life forms. As such, this review proposes that charting biodiversity futures is inherently normative and political. Drawing on diverse scholarship united under a banner of ‘futures thinking’ this review presents an array of methods, approaches and concepts that provide a foundation from which to consider research and decision-making that enables action in the context of contested and uncertain biodiversity futures.

Joint Estimation of Trajectory and Model Parameters for Single Particle Tracking of 3D Confined Diffusion Using the Double-Helix Point Spread Function.

Single particle tracking plays a significant role in biophysics through its ability to reveal dynamic mechanisms and physical properties of biological macromolecules inside living cells. The motion of these molecules can often be modeled as a confined diffusion. The standard paradigm in the biophysics community is to first estimate the trajectory of a particle and then use a technique such as the Mean Square Displacement or the Maximum Likelihood Estimation (MLE) to determine model parameters. These approaches, however, ignore the fact that localization and parameter estimation problems are coupled. We have previously introduced a framework based on optimal estimation theory to simultaneously do localization and parameter estimation. Here we build upon that work by expanding it to include a recent advance in imaging three dimensional motion, namely the Double-Helix (DH) engineered Point Spread Function (PSF). The DH-PSF encodes the axial position of the particle directly into the 2D image acquired by the camera mounted to the microscope. Our approach uses Expectation Maximization (EM) and Sequential Monte Carlo (SMC) to handle the nonlinearities in the observation and motion models. In this paper, we also improve upon the computational complexity of this scheme, using a Gaussian Particle Filter and Backward Simulation Particle Smoother in the SMC elements of the algorithm. We compare our scheme through simulation to state of the art methods based on localization using Gaussian fitting followed by MLE of the model parameters. These results show that our method outperforms GF-MLE at the low signal intensity levels common to biophysical experiments.

Angular Trapping of Spherical Janus Particles

AbstractDeveloping angular trapping methods, which enable optical tweezers to rotate a micronsized bead, is of great importance for studies of biomacromolecules in a wide range of torque‐generation processes. Here a novel controlled angular trapping method based on model composite Janus particles is reported, which consist of two hemispheres made of polystyrene and poly(methyl methacrylate). Through computational and experimental studies, the feasibility to control the rotation of a Janus particle in a linearly polarized laser trap is demonstrated. The results show that the Janus particle aligned its two hemispheres interface parallel to the laser propagation direction and polarization direction. The rotational state of the particle can be directly visualized by using a camera. The rotation of the Janus particle in the laser trap can be fully controlled in real time by controlling the laser polarization direction. The newly developed angular trapping technique has the great advantage of easy implementation and real‐time controllability. Considering the easy chemical preparation of Janus particles and implementation of the angular trapping, this novel method has the potential of becoming a general angular trapping method. It is anticipated that this new method will significantly broaden the availability of angular trapping in the biophysics community.

The data universe of structural biology.

The Protein Data Bank (PDB) has grown from a small data resource for crystallographers to a worldwide resource serving structural biology. The history of the growth of the PDB and the role that the community has played in developing standards and policies are described. This article also illustrates how other biophysics communities are collaborating with the worldwide PDB to create a network of interoperating data resources. This network will expand the capabilities of structural biology and enable the determination and archiving of increasingly complex structures.

Preface

The 3rd Annual Scientific Meeting on Medical Physics and Biophysics (PIT-FMB) in conjunction with the 17th South-East Asia Congress of Medical Physics (SEACOMP) was held in Bali, Indonesia from 8 to 10 August 2019. The annual event is aimed to gather medical physics and biophysics communities in Indonesia and South-East Asian region for sharing of knowledge, expertise, scientific discussions, cultural exchange and updates of medical physics activities. The event is also acts as a platform for the establishments of regional education, training and professional developments in medical physics and for the advancement in status and standard of practice of the medical physics profession in the region. The theme for this congress is “Improvement on Patient Care and Safety through the innovation in Medical Physics”.The congress was discussing four main themes: radiotherapy, diagnostic radiology, nuclear medicine and biophysics. The committee accepted 178 abstracts from more than 5 participating countries to be presented in the congress, 97 of which were listed as oral contributions and 81 were posters. The congress also had many invited lectures and workshops which discuss many in-depth topics related to the main themes, such as:• radiotherapy: quality assurance, dose calculation, patient safety issue, patient-specific IMRT treatment verification and quality management;• diagnostic radiology: optimization, technical and clinical image quality, multimodality molecular imaging and medical exposure in diagnostic imaging;• nuclear medicine: patient safety and optimization, radionuclide metrology, radiation safety and radiation protection;• biophysics: non-ionizing EMF, sensor for biomedical applications, monte carlo simulation for biological system and nanocellulose composite;List of PIT-FMB and SEACOMP 2019, Scientific Committee, Organising Committee and Reviewers, Organizers, Sponsorship Acknowledgements, Logos are available in this pdf.

Feedforward Control for Single Particle Tracking Synthetic Motion

Single particle tracking (SPT) is a method to study the transport of biomolecules with nanometer resolution. Unfortunately, recent reports show that systematic errors in position localization and uncertainty in model parameter estimates limits the utility of these techniques in studying biological processes. There is a need for an experimental method with a known ground-truth that tests the total SPT system (sample, microscope, algorithm) on both localization and estimation of model parameters. Synthetic motion is a known ground-truth method that moves a particle along a trajectory. This trajectory is a realization of a Markovian stochastic process that represents models of biomolecular transport. Here we describe a platform for creating synthetic motion using common equipment and well-known, simple methods that can be easily adopted by the biophysics community. In this paper we describe the synthetic motion system and calibration to achieve nanometer accuracy and precision. Steady state input-output characteristics are analyzed with both line scans and grid scans. The resulting relationship is described by an affine transformation, which is inverted and used as a prefilter. Model inverse feed forward control is used to increase the system bandwidth. The system model was identified from frequency response function measurements using an integrated stepped-sine with coherent demodulation built into the FPGA controller. Zero magnitude error tracking controller method was used to invert non-minimum phase zeros to achieve a stable discrete time feed forward filter.

Single cell force profiling of human myofibroblasts reveals a biophysical spectrum of cell states.

ABSTRACTMechanical force is a fundamental regulator of cell phenotype. Myofibroblasts are central mediators of fibrosis, a major unmet clinical need characterised by the deposition of excessive matrix proteins. Traction forces of myofibroblasts play a key role in remodelling the matrix and modulate the activities of embedded stromal cells. Here, we employ a combination of unsupervised computational analysis, cytoskeletal profiling and single cell traction force microscopy as a functional readout to uncover how the complex spatiotemporal dynamics and mechanics of living human myofibroblast shape sub-cellular profiling of traction forces in fibrosis. We resolve distinct biophysical communities of myofibroblasts, and our results provide a new paradigm for studying functional heterogeneity in human stromal cells.

TIPOLOGI PERUBAHAN TUTUPAN HUTAN DI KABUPATEN KUBU RAYA KALIMANTAN BARAT

Forest cover changes were influenced by many factors, some of which were biophysical characteristics, socio-economic conditions, and community cultural. The behavior of forest cover changes in each of Indonesia's regions varied, either its rate or its driving factors. The establishment of village typologies to categorize village administrative areas becomes important to see the driving factors that trigger forest change in each typology. The objective of this study was to develop the village typology and to identify the driving forces of forest cover change in each village in Kubu Raya Regency, West Kalimantan. The development of village typology was done by applying the clustering approach with standardized euclidean distances. Based on the proportion of forest in 2015, the study found that there are two village typologies within the study area with 81% OA. The study also recognized that the most significant driving forces of forest cover change in T1 were the distance from rivers (X2) and settlements (X3), whereas in T2 were the distance from roads (X1) and the edge of forest in 2015 (X9). The study concludes that the proximity from the center of the human activities holds a significant influence on the behavior of forest cover changes.

High-Field EPR Spectroscopic Characterization of Mn(II) Bound to the Bacterial Solute-Binding Proteins MntC and PsaA

During infection, the bacterial pathogens Staphylococcus aureus and Streptococcus pneumoniae employ ATP-binding cassette (ABC) transporters to acquire Mn(II), an essential nutrient, from the host environment. Staphylococcal MntABC and streptococcal PsaABC attract the attention of the biophysical and bacterial pathogenesis communities because of their established importance during infection. Previous biophysical examination of Mn(II)-MntC and Mn(II)-PsaA using continuous-wave (≈9 GHz) electron paramagnetic resonance (EPR) spectroscopy revealed broad, difficult-to-interpret spectra (Hadley et al. J. Am. Chem. Soc. 2018, 140, 110-113). Herein, we employ high-frequency (>90 GHz), high-field (>3 T) EPR spectroscopy to investigate the Mn(II)-binding sites of these proteins and determine the spin Hamiltonian parameters. Our analyses demonstrate that the zero-field splitting (ZFS) is large for Mn(II)-MntC and Mn(II)-PsaA at +2.72 and +2.87 GHz, respectively. The measured 55Mn hyperfine coupling values for Mn(II)-MntC and Mn(II)-PsaA of 241 and 236 MHz, respectively, demonstrate a more covalent interaction between Mn(II) and the protein compared to Mn(II) in aqueous solution (≈265 MHz). These studies indicate that MntC and PsaA bind Mn(II) in a similar coordination geometry. Comparison of the ZFS values determined herein with those ascertained for other Mn(II) proteins suggests that the Mn(II)-MntC and Mn(II)-PsaA coordination spheres are not five-coordinate in solution.

Agreement between Experimental and Simulated Circular Dichroic Spectra of a Positively Charged Peptide in Aqueous Solution and on Self-Assembled Monolayers.

Successfully immobilizing functional proteins on inorganic surfaces has long been a challenge to the biophysics and bioengineering communities. This is due, in part, to a lack of understanding of the effect of nonaqueous environments on protein structure from both experimental and computational perspectives. Because most experimental information about protein structure comes from the Protein Data Bank and is collected from an aqueous solvent environment, modern force fields for molecular dynamics (MD) simulations are parameterized against these data. The applicability of such force fields to biomolecules in different environments, including when in contact with surfaces and substrates, must be validated. Here, we present MD folding simulations of a highly charged peptide solvated in water, solvated in a solution of 2:1 t-BuOH/H2O and bound to the surface of a methyl-terminated self-assembled monolayer (SAM), and compare the structures predicted by these simulations to previously reported circular dichroism spectra. We show quantitative agreement between experiments and simulations of solvent- and surface-induced conformational changes of a positively charged peptide in these three environments. We show further that the surface-bound peptide must fold before chemically reacting with the surface. Finally, we demonstrate that a well-ordered SAM is critical to the folding process. These results will guide further simulations of peptides and proteins in diverse and complex environments.

A Formulation for Fluid-Structure Interactions in febio Using Mixture Theory.

Many physiological systems involve strong interactions between fluids and solids, posing a significant challenge when modeling biomechanics. The objective of this study was to implement a fluid-structure interaction (FSI) solver in the free, open-source finite element code FEBio, that combined the existing solid mechanics and rigid body dynamics solver with a recently developed computational fluid dynamics (CFD) solver. A novel Galerkin-based finite element FSI formulation was introduced based on mixture theory, where the FSI domain was described as a mixture of fluid and solid constituents that have distinct motions. The mesh was defined on the solid domain, specialized to have zero mass, negligible stiffness, and zero frictional interactions with the fluid, whereas the fluid was modeled as isothermal and compressible. The mixture framework provided the foundation for evaluating material time derivatives in a material frame for the solid and in a spatial frame for the fluid. Similar to our recently reported CFD solver, our FSI formulation did not require stabilization methods to achieve good convergence, producing a compact set of equations and code implementation. The code was successfully verified against benchmark problems from the FSI literature and an analytical solution for squeeze-film lubrication. It was validated against experimental measurements of the flow rate in a peristaltic pump and illustrated using non-Newtonian blood flow through a bifurcated carotid artery with a thick arterial wall. The successful formulation and implementation of this FSI solver enhance the multiphysics modeling capabilities in febio relevant to the biomechanics and biophysics communities.

Automated Markov state models for molecular dynamics simulations of aggregation and self-assembly.

Markov state models have become popular in the computational biochemistry and biophysics communities as a technique for identifying stationary and kinetic information of protein dynamics from molecular dynamics simulation data. In this paper, we extend the applicability of automated Markov state modeling to simulation data of molecular self-assembly and aggregation by constructing collective coordinates from molecular descriptors that are invariant to permutations of molecular indexing. Understanding molecular self-assembly is of critical importance if we want to deepen our understanding of neurodegenerative diseases where the aggregation of misfolded or disordered proteins is thought to be the main culprit. As a proof of principle, we demonstrate our Markov state model technique on simulations of the KFFE peptide, a subsequence of Alzheimer's amyloid-β peptide and one of the smallest peptides known to aggregate into amyloid fibrils in vitro. We investigate the different stages of aggregation up to tetramerization and show that the Markov state models clearly map out the different aggregation pathways. Of note is that disordered and β-sheet oligomers do not interconvert, leading to separate pathways for their formation. This suggests that amyloid aggregation of KFFE occurs via ordered aggregates from the very beginning. The code developed here is freely available as a Jupyter notebook called TICAgg, which can be used for the automated analysis of any self-assembling molecular system, protein, or otherwise.

Micropipette force sensors for in vivo force measurements on single cells and multicellular microorganisms.

Measuring forces from the piconewton to millinewton range is of great importance for the study of living systems from a biophysical perspective. The use of flexible micropipettes as highly sensitive force probes has become established in the biophysical community, advancing our understanding of cellular processes and microbial behavior. The micropipette force sensor (MFS) technique relies on measurement of the forces acting on a force-calibrated, hollow glass micropipette by optically detecting its deflections. The MFS technique covers a wide micro- and mesoscopic regime of detectable forces (tens of piconewtons to millinewtons) and sample sizes (micrometers to millimeters), does not require gluing of the sample to the cantilever, and allows simultaneous optical imaging of the sample throughout the experiment. Here, we provide a detailed protocol describing how to manufacture and calibrate the micropipettes, as well as how to successfully design, perform, and troubleshoot MFS experiments. We exemplify our approach using the model nematode Caenorhabditis elegans, but by following this protocol, a wide variety of living samples, ranging from single cells to multicellular aggregates and millimeter-sized organisms, can be studied in vivo, with a force resolution as low as 10 pN. A skilled (under)graduate student can master the technique in ~1-2 months. The whole protocol takes ~1-2 d to finish.

Thermodynamics of helix formation in small peptides of varying length in vacuo, in implicit solvent, and in explicit solvent.

Helix formation plays a critical role in the functionality of proteins. Various biological processes such as protein-ligand, protein-protein, and protein-nucleotide interactions are strongly influenced by the conformational stability of peptides. Small peptides represent ideal models to study the process of helix formation due to their small size and simple structures. As is widely known in the biophysical community, different amino acids have different propensities for helix formation. In this work, we used model peptides to study the peptide-length dependence and the sequence dependence of the thermodynamic profiles along the helix formation pathway in vacuo and in water. The peptides showed interesting unfolding behavior in vacuo, as this process was found to be protonation-state dependent, sequence-length dependent, and to change when residues in the peptide were mutated. Ionizable group protonation alters helix propensity by changing the degree of charge-charge repulsion in the peptide. Longer sequences tend to form more hydrogen bonds and are more likely to form helical structures. Mutation of an alanine residue to another naturally occurring amino acid changes the interactions within the peptide, which in turn alters its helix-forming tendency. By contrast, solvation leads to the generation of protein-solvent hydrogen bonds, which compensate for the energy penalty associated with the deformation of backbone hydrogen bonds in the extended conformation. Flat free-energy profiles were obtained for all mutated peptides of various lengths. Although several implicit-solvent models were able to reproduce free energies of helix formation in explicit solvent, the conformational ensembles varied with the solvent model applied, particularly in terms of the populations of secondary structures and the formation of backbone hydrogen bonds. Also, due to the absence of explicit descriptions of solvent molecules and thus protein-solvent hydrogen bonds in implicit-solvent models, they did not yield accurate hydrogen-bonding profiles.