Advancing Biophysics Using DNA Origami

2021 ◽  
Vol 50 (1) ◽  
Author(s):  
Wouter Engelen ◽  
Hendrik Dietz
Keyword(s):  
Electron Microscopy ◽  
Lipid Membranes ◽  
Force Measurement ◽  
Experimental Methods ◽  
Dna Origami ◽  
Added Value ◽  
Annual Review ◽  
Publication Date ◽  
Complex Environments ◽  
Positioning Devices

DNA origami enables the bottom-up construction of chemically addressable, nanoscale objects with user-defined shapes and tailored functionalities. As such, not only can DNA origami objects be used to improve existing experimental methods in biophysics, but they also open up completely new avenues of exploration. In this review, we discuss basic biophysical concepts that are relevant for prospective DNA origami users. We summarize biochemical strategies for interfacing DNA origami with biomolecules of interest. We describe various applications of DNA origami, emphasizing the added value or new biophysical insights that can be generated: rulers and positioning devices, force measurement and force application devices, alignment supports for structural analysis for biomolecules in cryogenic electron microscopy and nuclear magnetic resonance, probes for manipulating and interacting with lipid membranes, and programmable nanopores. We conclude with some thoughts on so-far little explored opportunities for using DNA origami in more complex environments such as the cell or even organisms. Expected final online publication date for the Annual Review of Biophysics, Volume 50 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Molecular Force Measurement with Tension Sensors

2021 ◽  
Vol 50 (1) ◽  
Author(s):  
Lisa S. Fischer ◽  
Srishti Rangarajan ◽  
Tanmay Sadhanasatish ◽  
Carsten Grashoff
Keyword(s):  
Molecular Mechanisms ◽  
Force Measurement ◽  
Annual Review ◽  
Publication Date ◽  
Mechanical Forces ◽  
Biophysical Parameters ◽  
Cellular Mechanotransduction ◽  
Molecular Force ◽  
Molecular Forces ◽  
Physical Principles

The ability of cells to generate mechanical forces, but also to sense, adapt to, and respond to mechanical signals, is crucial for many developmental, postnatal homeostatic, and pathophysiological processes. However, the molecular mechanisms underlying cellular mechanotransduction have remained elusive for many decades, as techniques to visualize and quantify molecular forces across individual proteins in cells were missing. The development of genetically encoded molecular tension sensors now allows the quantification of piconewton-scale forces that act upon distinct molecules in living cells and even whole organisms. In this review, we discuss the physical principles, advantages, and limitations of this increasingly popular method. By highlighting current examples from the literature, we demonstrate how molecular tension sensors can be utilized to obtain access to previously unappreciated biophysical parameters that define the propagation of mechanical forces on molecular scales. We discuss how the methodology can be further developed and provide a perspective on how the technique could be applied to uncover entirely novel aspects of mechanobiology in the future. Expected final online publication date for the Annual Review of Biophysics, Volume 50 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Cryogenic Super-Resolution Fluorescence and Electron Microscopy Correlated at the Nanoscale

2021 ◽  
Vol 72 (1) ◽  
Author(s):  
Peter D. Dahlberg ◽  
W.E. Moerner
Keyword(s):  
Electron Microscopy ◽  
Single Molecule ◽  
Electron Tomography ◽  
Light And Electron Microscopy ◽  
Super Resolution ◽  
Nanometer Scale ◽  
Annual Review ◽  
Publication Date ◽  
Fluorescence And Electron Microscopy ◽  
Cellular Context

We review the emerging method of super-resolved cryogenic correlative light and electron microscopy (srCryoCLEM). Super-resolution (SR) fluorescence microscopy and cryogenic electron tomography (CET) are both powerful techniques for observing subcellular organization, but each approach has unique limitations. The combination of the two brings the single-molecule sensitivity and specificity of SR to the detailed cellular context and molecular scale resolution of CET. The resulting correlative data is more informative than the sum of its parts. The correlative images can be used to pinpoint the positions of fluorescently labeled proteins in the high-resolution context of CET with nanometer-scale precision and/or to identify proteins in electron-dense structures. The execution of srCryoCLEM is challenging and the approach is best described as a method that is still in its infancy with numerous technical challenges. In this review, we describe state-of-the-art srCryoCLEM experiments, discuss the most pressing challenges, and give a brief outlook on future applications. Expected final online publication date for the Annual Review of Physical Chemistry, Volume 72 is April 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Preparing Better Samples for Cryo–Electron Microscopy: Biochemical Challenges Do not End with Isolation and Purification

2021 ◽  
Vol 90 (1) ◽  
Author(s):  
Robert M. Glaeser
Keyword(s):  
Electron Microscopy ◽  
High Resolution Electron Microscopy ◽  
Effective Control ◽  
Annual Review ◽  
Publication Date ◽  
Biological Macromolecules ◽  
Isolation And Purification ◽  
Cryo Electron Microscopy ◽  
Extreme Risk ◽  
Resolution Electron

The preparation of extremely thin samples, which are required for high-resolution electron microscopy, poses extreme risk of damaging biological macromolecules due to interactions with the air-water interface. Although the rapid increase in the number of published structures initially gave little indication that this was a problem, the search for methods that substantially mitigate this hazard is now intensifying. The two main approaches under investigation are ( a) immobilizating particles onto structure-friendly support films and ( b) reducing the length of time during which such interactions may occur. While there is little possibility of outrunning diffusion to the interface, intentional passivation of the interface may slow the process of adsorption and denaturation. In addition, growing attention is being given to gaining more effective control of the thickness of the sample prior to vitrification. Expected final online publication date for the Annual Review of Biochemistry, Volume 90 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Enzymology and Dynamics by Cryogenic Electron Microscopy

2021 ◽  
Vol 51 (1) ◽  
Author(s):  
Ming-Daw Tsai ◽  
Wen-Jin Wu ◽  
Meng-Chiao Ho
Keyword(s):  
Electron Microscopy ◽  
Protein Complexes ◽  
Specific Protein ◽  
Dynamic Processes ◽  
Annual Review ◽  
Publication Date ◽  
X Ray Crystallography ◽  
Multiple Dimensions ◽  
Specific Proteins ◽  
Future Potential

Cryogenic electron microscopy (cryo-EM) has revolutionized the field of structural biology, particularly in solving the structures of large protein complexes or cellular machineries that play important biological functions. This review focuses on the contribution and future potential of cryo-EM in related emerging applications—enzymatic mechanisms and dynamic processes. Work on these subjects can benefit greatly from the capability of cryo-EM to solve the structures of specific protein complexes in multiple conditions, including variations in the buffer condition, ligands, and temperature, and to capture multiple conformational states, conformational change intermediates, and reaction intermediates. These studies can expand the structural landscape of specific proteins or protein complexes in multiple dimensions and drive new advances in the fields of enzymology and dynamic processes. The advantages and complementarity of cryo-EM relative to X-ray crystallography and nuclear magnetic resonance with regard to these applications are also addressed. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Developmental Perspectives on the Study of Persons with Intellectual Disability

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Jacob A. Burack ◽  
David W. Evans ◽  
Natalie Russo ◽  
Jenilee-Sarah Napoleon ◽  
Karen J. Goldman ◽  
...  
Keyword(s):  
Intellectual Disability ◽  
Life Span ◽  
Diagnostic Criteria ◽  
Adaptive Behavior ◽  
Clinical Psychology ◽  
Online Publication ◽  
Annual Review ◽  
Publication Date ◽  
Complex Environments ◽  
Heterogenous Group

Developmental approaches provide inclusive, universal, and methodologically rigorous frameworks for studying persons with intellectual disability (ID). This is an exceptionally heterogenous group with regard to etiology, genotype, and phenotype that simply shares the traditional diagnostic criteria, typically a score of two standard deviations below the population mean of 100 on standardized IQ tests and deficits in adaptive behavior. We trace the foundational, conceptual, and methodological roots of developmental approaches and highlight ways that these and more recent iterations continue to be central to advances in the increasingly nuanced study of persons with ID. This work is premised on the consideration of specific etiological and subetiological groups across and between different domains of functioning within the context of familial and complex environments throughout the life span. We highlight the potential contributions of advances in behavioral methodologies, genomics, and neuroscience when considered within universal and hierarchic frameworks based on development. Expected final online publication date for the Annual Review of Clinical Psychology, Volume 17 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Towards Iron-Titanium Oxide Nanostructures from Ecuadorian Black Mineral Sands

Minerals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 122
Author(s):  
Karina J. Lagos ◽  
Bojan A. Marinkovic ◽  
Alexis Debut ◽  
Karla Vizuete ◽  
Víctor H. Guerrero ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Titanium Oxide ◽  
Low Cost ◽  
Mineral Resources ◽  
Added Value ◽  
Secondary Phases ◽  
Hydrothermal Route ◽  
Oxide Nanostructures ◽  
Transmission Electron ◽  
Pre Treatment

Ecuadorian black mineral sands were used as starting material for the production of iron-titanium oxide nanostructures. For this purpose, two types of mineral processing were carried out, one incorporating a pre-treatment before conducting an alkaline hydrothermal synthesis (NaOH 10 M at 180 °C for 72 h), and the other prescinding this first step. Nanosheet-assembled flowers and nanoparticle agglomerates were obtained from the procedure including the pre-treatment. Conversely, nanobelts and plate-like particles were prepared by the single hydrothermal route. The nanoscale features of the product morphologies were observed by scanning electron microscopy (SEM) and transmission electron microscopy (TEM) analyses. The ilmenite and hematite molar fractions, within the ilmenite-hematite solid solution, in the as-synthetized samples were estimated by Brown’s approach using the computed values of unit-cell volumes from Le Bail adjustments of X-ray powder diffraction (XRPD) patterns. The resulting materials were mainly composed of Fe-rich ilmenite-hematite solid solutions (hematite molar contents ≥0.6). Secondary phases, which possibly belong to lepidocrocite-like or corrugated titanate structures, were also identified. The current study demonstrated the feasibility of employing Ecuadorian mineral resources as low-cost precursors to synthesize high-added-value nanostructures with promising applications in several fields.

Endogenous Retroviruses Drive Resistance and Promotion of Exogenous Retroviral Homologs

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Elliott S. Chiu ◽  
Sue VandeWoude
Keyword(s):  
Immune Modulation ◽  
Viral Infections ◽  
Viral Evolution ◽  
Endogenous Retroviruses ◽  
Annual Review ◽  
Publication Date ◽  
Biological Functions ◽  
Self Tolerance ◽  
Vertebrate Hosts ◽  
Insight Into

Endogenous retroviruses (ERVs) serve as markers of ancient viral infections and provide invaluable insight into host and viral evolution. ERVs have been exapted to assist in performing basic biological functions, including placentation, immune modulation, and oncogenesis. A subset of ERVs share high nucleotide similarity to circulating horizontally transmitted exogenous retrovirus (XRV) progenitors. In these cases, ERV–XRV interactions have been documented and include ( a) recombination to result in ERV–XRV chimeras, ( b) ERV induction of immune self-tolerance to XRV antigens, ( c) ERV antigen interference with XRV receptor binding, and ( d) interactions resulting in both enhancement and restriction of XRV infections. Whereas the mechanisms governing recombination and immune self-tolerance have been partially determined, enhancement and restriction of XRV infection are virus specific and only partially understood. This review summarizes interactions between six unique ERV–XRV pairs, highlighting important ERV biological functions and potential evolutionary histories in vertebrate hosts. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 9 is February 16, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Advancing Socioeconomic Rights Through Interdisciplinary Factfinding: Opportunities and Challenges

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Sarah Knuckey ◽  
Joshua D. Fisher ◽  
Amanda M. Klasing ◽  
Tess Russo ◽  
Margaret L. Satterthwaite
Keyword(s):  
Human Rights ◽  
Mixed Methods ◽  
Social Science ◽  
Science Volume ◽  
Lessons Learned ◽  
Limited Resources ◽  
Annual Review ◽  
Publication Date ◽  
Socioeconomic Rights ◽  
Human Rights Movement

The human rights movement is increasingly using interdisciplinary, multidisciplinary, mixed-methods, and quantitative factfinding. There has been too little analysis of these shifts. This article examines some of the opportunities and challenges of these methods, focusing on the investigation of socioeconomic human rights. By potentially expanding the amount and types of evidence available, factfinding's accuracy and persuasiveness can be strengthened, bolstering rights claims. However, such methods can also present significant challenges and may pose risks in individual cases and to the human rights movement generally. Interdisciplinary methods can be costly in human, financial, and technical resources; are sometimes challenging to implement; may divert limited resources from other work; can reify inequalities; may produce “expertise” that disempowers rightsholders; and could raise investigation standards to an infeasible or counterproductive level. This article includes lessons learned and questions to guide researchers and human rights advocates considering mixed-methods human rights factfinding. Expected final online publication date for the Annual Review of Law and Social Science, Volume 17 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Conversation and Culture

2021 ◽  
Vol 50 (1) ◽  
Author(s):  
Simeon Floyd
Keyword(s):  
Conversation Analysis ◽  
Quantitative Methods ◽  
Sequential Analysis ◽  
Contemporary Literature ◽  
Annual Review ◽  
Publication Date ◽  
Face To Face ◽  
Qualitative And Quantitative Methods ◽  
Language Studies ◽  
Speech Communities

Conversation analysis is a method for the systematic study of interaction in terms of a sequential turn-taking system. Research in conversation analysis has traditionally focused on speakers of English, and it is still unclear to what extent the system observed in that research applies to conversation more generally around the world. However, as this method is now being applied to conversation in a broader range of languages, it is increasingly possible to address questions about the nature of interactional diversity across different speech communities. The approach of pragmatic typology first applies sequential analysis to conversation from different speech communities and then compares interactional patterns in ways analogous to how traditional linguistic typology compares morphosyntax. This article discusses contemporary literature in pragmatic typology, including single-language studies and multilanguage comparisons reflecting both qualitative and quantitative methods. This research finds that microanalysis of face-to-face interaction can identify both universal trends and culture-specific interactional tendencies. Expected final online publication date for the Annual Review of Anthropology, Volume 50 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Mechanical Patterning in Animal Morphogenesis

2021 ◽  
Vol 37 (1) ◽  
Author(s):  
Yonit Maroudas-Sacks ◽  
Kinneret Keren
Keyword(s):  
Pattern Formation ◽  
Large Scale ◽  
Coarse Grained ◽  
Annual Review ◽  
Publication Date ◽  
Biochemical Processes ◽  
Substantial Progress ◽  
Biological Pattern Formation ◽  
Effective Theories ◽  
Biochemical Signals

Morphogenesis is one of the most remarkable examples of biological pattern formation. Despite substantial progress in the field, we still do not understand the organizational principles responsible for the robust convergence of the morphogenesis process across scales to form viable organisms under variable conditions. Achieving large-scale coordination requires feedback between mechanical and biochemical processes, spanning all levels of organization and relating the emerging patterns with the mechanisms driving their formation. In this review, we highlight the role of mechanics in the patterning process, emphasizing the active and synergistic manner in which mechanical processes participate in developmental patterning rather than merely following a program set by biochemical signals. We discuss the value of applying a coarse-grained approach toward understanding this complex interplay, which considers the large-scale dynamics and feedback as well as complementing the reductionist approach focused on molecular detail. A central challenge in this approach is identifying relevant coarse-grained variables and developing effective theories that can serve as a basis for an integrated framework for understanding this remarkable pattern-formation process. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Sign in / Sign up

Export Citation Format

Share Document