scholarly journals FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Eitan Lerner ◽  
Anders Barth ◽  
Jelle Hendrix ◽  
Benjamin Ambrose ◽  
Victoria Birkedal ◽  
...  
Keyword(s):  
Structural Biology ◽  
Single Molecule ◽  
Open Science ◽  
Quantitative Information ◽  
Methodological Issues ◽  
Biomolecular Structure ◽  
Science Practices ◽  
Structure And Dynamics ◽  
Single Molecule Fret ◽  
Current State

Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics. The recent efforts include blind tests to assess the accuracy and the precision of smFRET experiments among different labs using various procedures. These multi-lab studies have led to the development of smFRET procedures and documentation, which are important when submitting entries into the archiving system for integrative structure models, PDB-Dev. This position paper describes the current ‘state of the art’ from different perspectives, points to unresolved methodological issues for quantitative structural studies, provides a set of ‘soft recommendations’ about which an emerging consensus exists, and lists openly available resources for newcomers and seasoned practitioners. To make further progress, we strongly encourage ‘open science’ practices.

scholarly journals The past, present, and future of ego depletion

2019 ◽  
Author(s):  
Michael Inzlicht ◽  
Malte Friese
Keyword(s):  
Social Psychology ◽  
Ego Depletion ◽  
Open Science ◽  
Science Practices ◽  
Current State ◽  
Scientific Status ◽  
Replication Crisis ◽  
History Of ◽  
Controversial Topic ◽  
Mere Existence

At the center of social psychology just a few years ago, ego depletion is now widely seen as a controversial topic, one of the chief victims of the replication crisis. Despite over 600 studies of apparent support, many are now asking if ego depletion is even real. Here, we comment on the articles included in this Special Issue: Ego Depletion. Specifically, we delineate the contributions and limitations of these articles by embedding them in a brief history of ego depletion, describing the current state of uncertainty about ego depletion’s scientific status, and outlining necessary steps for the study of ego depletion to have a healthy future. To us, the most troubling aspect of this controversy is not what is suggests about ego depletion; but what it suggests about social psychology more broadly. If the mere existence of ego depletion is seriously doubted by many, what can be confidently regarded as real in social psychology? By increasing the precision of our theories, continuously validating our manipulations and measures, and practicing the full suite of open science practices we have the potential to identify legitimate and robust effects and build a cumulative and trustworthy psychological science.

scholarly journals Assessment of 3D MINFLUX data for quantitative structural biology in cells

2021 ◽  
Author(s):  
Kirti Prakash ◽  
Alistair Curd
Keyword(s):  
Quantitative Analysis ◽  
Structural Biology ◽  
Single Molecule ◽  
Structural Features ◽  
Localization Microscopy ◽  
Current State ◽  
New Development ◽  
Very High ◽  
Single Molecule Localization Microscopy ◽  
In Cells

MINFLUX is a promising new development in single-molecule localization microscopy, claiming a resolution of 1-3 nm in living and fixed biological specimens. While MINFLUX can achieve very high localisation precision, quantitative analysis of reported results leads us to dispute the resolution claim and question reliability for imaging sub-100-nm structural features, in its current state.

scholarly journals DeepFRET: Rapid and automated single molecule FRET data classification using deep learning

2020 ◽  
Author(s):  
Johannes Thomsen ◽  
Magnus B. Sletfjerding ◽  
Stefano Stella ◽  
Bijoya Paul ◽  
Simon Bo Jensen ◽  
...  
Keyword(s):  
Deep Learning ◽  
Structural Biology ◽  
Single Molecule ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Ground Truth ◽  
Real Data ◽  
Ground Truth Data ◽  
Single Molecule Fret ◽  
Human Operators

AbstractSingle molecule Förster Resonance energy transfer (smFRET) is a mature and adaptable method for studying the structure of biomolecules and integrating their dynamics into structural biology. The development of high throughput methodologies and the growth of commercial instrumentation have outpaced the development of rapid, standardized, and fully automated methodologies to objectively analyze the wealth of produced data. Here we present DeepFRET, an automated standalone solution based on deep learning, where the only crucial human intervention in transiting from raw microscope images to histogram of biomolecule behavior, is a user-adjustable quality threshold. Integrating all standard features of smFRET analysis, DeepFRET will consequently output common kinetic information metrics for biomolecules. We validated the utility of DeepFRET by performing quantitative analysis on simulated, ground truth, data and real smFRET data. The accuracy of classification by DeepFRET outperformed human operators and current commonly used hard threshold and reached >95% precision accuracy only requiring a fraction of the time (<1% as compared to human operators) on ground truth data. Its flawless and rapid operation on real data demonstrates its wide applicability. This level of classification was achieved without any preprocessing or parameter setting by human operators, demonstrating DeepFRET’s capacity to objectively quantify biomolecular dynamics. The provided a standalone executable based on open source code capitalises on the widespread adaptation of machine learning and may contribute to the effort of benchmarking smFRET for structural biology insights.

scholarly journals Decoding the Structural Dynamics and Conformational Alternations of DNA Secondary Structures by Single-Molecule FRET Microspectroscopy

2021 ◽  
Vol 8 ◽  
Author(s):  
Debolina Bandyopadhyay ◽  
Padmaja P. Mishra
Keyword(s):  
Single Molecule ◽  
Double Helix ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Secondary Structures ◽  
Quantitative Information ◽  
High Rate ◽  
Single Molecule Fret ◽  
Ensemble Techniques ◽  
Biological Phenomena

In addition to the canonical double helix form, DNA is known to be extrapolated into several other secondary structural patterns involving themselves in inter- and intramolecular type hydrogen bonding. The secondary structures of nucleic acids go through several stages of multiple, complex, and interconvertible heterogeneous conformations. The journey of DNA through these conformers has significant importance and has been monitored thoroughly to establish qualitative and quantitative information about the transition between the unfolded, folded, misfolded, and partially folded states. During this structural interconversion, there always exist specific populations of intermediates, which are short-lived or sometimes even do not accumulate within a heterogeneous population and are challenging to characterize using conventional ensemble techniques. The single-molecule FRET(sm-FRET) microspectroscopic method has the advantages to overcome these limitations and monitors biological phenomena transpiring at a measurable high rate and balanced stochastically over time. Thus, tracing the time trajectory of a particular molecule enables direct measurement of the rate constant of each transition step, including the intermediates that are hidden in the ensemble level due to their low concentrations. This review is focused on the advantages of the employment of single-molecule Forster’s resonance energy transfer (sm-FRET), which is worthwhile to access the dynamic architecture and structural transition of various secondary structures that DNA adopts, without letting the donor of one molecule to cross-talk with the acceptor of any other. We have emphasized the studies performed to explore the states of folding and unfolding of several nucleic acid secondary structures, for example, the DNA hairpin, Holliday junction, G-quadruplex, and i-motif.

scholarly journals A Hydrologist's Guide to Open Science

2021 ◽  
Author(s):  
Caitlyn A. Hall ◽  
Sheila M. Saia ◽  
Andrea L. Popp ◽  
Nilay Dogulu ◽  
Stanislaus J. Schymanski ◽  
...  
Keyword(s):  
Open Access ◽  
Scientific Community ◽  
Open Science ◽  
Reproducible Research ◽  
Research Experiences ◽  
Science Practices ◽  
Practical Guide ◽  
Current State ◽  
Research And Education

Abstract. Open, accessible, reusable, and reproducible hydrologic research can have a significant impact on the scientific community and broader society. While more individuals and organizations within the hydrology community are embracing open science practices, technical (e.g., limited coding experience), resource (e.g., open access fees), and social (e.g., fear of being scooped) challenges remain. Furthermore, there are a growing number of constantly evolving open science tools, resources, and initiatives that can seem overwhelming. These challenges and the ever-evolving nature of the open science landscape may seem insurmountable for hydrologists interested in pursuing open science. Therefore, we propose general Open Hydrology Principles to guide individual and community progress toward open science for research and education and the Open Hydrology Practical Guide to improve the accessibility of currently available tools and approaches. We aim to inform and empower hydrologists as they transition to open, accessible, reusable, and reproducible research. We discuss the benefits as well as common open science challenges and how hydrologists can overcome them. The Open Hydrology Principles and Open Hydrology Practical Guide reflect our knowledge of the current state of open hydrology; we recognize that recommendations and suggestions will evolve and expand with emerging open science infrastructures, workflows, and research experiences. Therefore, we encourage hydrologists all over the globe to join in and help advance open science by contributing to the living version of this document and by sharing open hydrology resources in the community-supported repository (https://open-hydrology.github.io).

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