717 results match your criteria Biophysical reviews[Journal]


The RNA-binding fragile-X mental retardation protein and its role beyond the brain.

Biophys Rev 2020 Jul 11. Epub 2020 Jul 11.

Discipline of Pathology and Bosch Institute, The University of Sydney, Level 4 West, Charles Perkins Centre D17, Sydney, NSW, 2006, Australia.

It is well-established that variations of a CGG repeat expansion in the gene FMR1, which encodes the fragile-X mental retardation protein (FMRP), cause the neurocognitive disorder, fragile-X syndrome (FXS). However, multiple observations suggest a general and complex regulatory role of FMRP in processes outside the brain: (1) FMRP is ubiquitously expressed in the body, suggesting it functions in multiple organ systems; (2) patients with FXS can exhibit a physical phenotype that is consistent with an underlying abnormality in connective tissue; (3) different CGG repeat expansion lengths in FMR1 result in different clinical outcomes due to different pathogenic mechanisms; (4) the function of FMRP as an RNA-binding protein suggests it has a general regulatory role. This review details the complex nature of FMRP and the different CGG repeat expansion lengths and the evidence supporting the essential role of the protein in a variety of biological and pathological processes. Read More

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http://dx.doi.org/10.1007/s12551-020-00730-4DOI Listing

Disease mutations in striated muscle myosins.

Biophys Rev 2020 Jul 10. Epub 2020 Jul 10.

School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.

Over 1000 disease-causing missense mutations have been found in human β-cardiac, α-cardiac, embryonic and adult fast myosin 2a myosin heavy chains. Most of these are found in human β-cardiac myosin heavy chain. Mutations in β-cardiac myosin cause hypertrophic cardiomyopathy predominantly, whereas those in α-cardiac are associated with many types of heart disease, of which the most common is dilated cardiomyopathy. Read More

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http://dx.doi.org/10.1007/s12551-020-00721-5DOI Listing

Synthetic biology approaches to dissecting linear motor protein function: towards the design and synthesis of artificial autonomous protein walkers.

Biophys Rev 2020 Jul 10. Epub 2020 Jul 10.

School of Physics, University of New South Wales, Sydney, NSW, 2052, Australia.

Molecular motors and machines are essential for all cellular processes that together enable life. Built from proteins with a wide range of properties, functionalities and performance characteristics, biological motors perform complex tasks and can transduce chemical energy into mechanical work more efficiently than human-made combustion engines. Sophisticated studies of biological protein motors have provided many structural and biophysical insights and enabled the development of models for motor function. Read More

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http://dx.doi.org/10.1007/s12551-020-00717-1DOI Listing

Cris dos Remedios: Sydney Heart Bank and scientific mentorship beyond 2010.

Authors:
Amy Li

Biophys Rev 2020 Jul 10. Epub 2020 Jul 10.

Department of Pharmacy & Biomedical Sciences, La Trobe University, Bendigo, VIC, 3552, Australia.

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http://dx.doi.org/10.1007/s12551-020-00733-1DOI Listing

Nanomolar ATP binding to single myosin cross-bridges in rigor: a molecular approach to studying myosin ATP kinetics using single human cardiomyocytes.

Biophys Rev 2020 Jul 9. Epub 2020 Jul 9.

Victor Chang Cardiac Research Institute, Molecular Cardiology Group, Darlinghurst, NSW, 2020, Australia.

Our knowledge in the field of cardiac muscle and associated cardiomyopathies has been evolving incrementally over the past 60 years and all was possible due to the parallel progress in techniques and methods allowing to take a fresh glimpse at an old problem. Here, we describe an exciting tool used to examine the various states of the human cardiac myosin at the single molecule level. By imaging single Alexa-ATP binding to permeabilised cardiomyocytes using total internal reflection fluorescence (TIRF) microscopy, we are able to acquire large populations of events in a short timeframe (~ 5000 sites in ~ 10 min) and measure each binding event with high spatio-temporal resolution. Read More

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http://dx.doi.org/10.1007/s12551-020-00716-2DOI Listing

A career in biophysics.

Biophys Rev 2020 Jul 9. Epub 2020 Jul 9.

Molecular Cardiology and Biophysics, Victor Chang Cardiac Research Institute, Lowy Packer Building, 405 Liverpool Street, Darlinghurst, 2020, Australia.

My career in science started with my PhD under Professor Darcy Gilmour at the University of Sydney. I quickly learned his iconoclastic ways and completed the degree in early 1969 in just over three years. Professor Charles Birch was the Head of Zoology and had been watching my progress and offered me a position as Lecturer as soon as my PhD was submitted. Read More

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http://dx.doi.org/10.1007/s12551-020-00714-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7346851PMC

Cris never left you wondering about where you stood! His motto was: Just do it!

Biophys Rev 2020 Jul 8. Epub 2020 Jul 8.

Faculty of Medicine and Health, School of Medical Sciences, Discipline of Pathology, The University of Sydney, Sydney, NSW, 2006, Australia.

In this commentary, we reflect on our experiences being PhD students of Prof. Cris dos Remedios in the Muscle Research Unit at The University of Sydney at the turn of the new millennium. Cris was/is an example of a fine scientist and a great academic mentor for us and so many others (scientists, academics, surgeons, medical doctors and health professionals) who carry the legacy and traditions of Cris dos Remedios into the future. Read More

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http://dx.doi.org/10.1007/s12551-020-00728-yDOI Listing

Fond memories of my PhD research in Professor Cris dos Remedios' laboratory.

Biophys Rev 2020 Jul 8. Epub 2020 Jul 8.

Department of Dermatology, The Canberra Hospital, Canberra, ACT, Australia.

I completed my PhD in 2013 under the supervision of Prof Cristobal G. dos Remedios, Department of Anatomy and Histology, The University of Sydney. His guidance and exemplary scientific standard in his laboratory ignited an insatiable scientific curiosity that continuously pushes me towards new knowledge through my own research. Read More

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http://dx.doi.org/10.1007/s12551-020-00727-zDOI Listing

'Muscle superman' Cristobal Guillermo dos Remedios: five decades of endless energy.

Authors:
Filip Braet

Biophys Rev 2020 Jul 8. Epub 2020 Jul 8.

Australian Centre for Microscopy & Microanalysis and School of Medical Sciences (Discipline of Anatomy and Histology), The University of Sydney, Camperdown, NSW, 2006, Australia.

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http://dx.doi.org/10.1007/s12551-020-00718-0DOI Listing

Double the trouble: giant proteins with dual kinase activity in the heart.

Biophys Rev 2020 Jul 8. Epub 2020 Jul 8.

Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St, Baltimore, MD, 21201, USA.

Obscurin and its homolog, striated muscle preferentially expressed gene (SPEG), constitute a unique group of proteins abundantly expressed in striated muscles that contain two tandemly arranged MLCK-like kinases. The physiological significance of the dual kinase motifs is largely understudied; however, a collection of recent studies characterizing their binding interactions, putative targets, and disease-linked mutations have begun to shed light on their potential roles in muscle pathophysiology. Specifically, obscurin kinase 1 is proposed to regulate cardiomyocyte adhesion via phosphorylating N-cadherin, whereas SPEG kinases 1 and 2 regulate Ca cycling by phosphorylating junctophilin-2 and the sarcoendoplasmic Ca ATPase 2 (SERCA2). Read More

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http://dx.doi.org/10.1007/s12551-020-00715-3DOI Listing

Challenges and emerging systems biology approaches to discover how the human gut microbiome impact host physiology.

Biophys Rev 2020 Jul 7. Epub 2020 Jul 7.

School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong.

Research in the human gut microbiome has bloomed with advances in next generation sequencing (NGS) and other high-throughput molecular profiling technologies. This has enabled the generation of multi-omics datasets which holds promises for big data-enabled knowledge acquisition in the form of understanding the normal physiological and pathological involvement of gut microbiomes. Ample evidence suggests that distinct microbial compositions in the human gut are associated with different diseases. Read More

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http://dx.doi.org/10.1007/s12551-020-00724-2DOI Listing

IL-34, IL-36 and IL-38 in colorectal cancer-key immunoregulators of carcinogenesis.

Biophys Rev 2020 Jul 7. Epub 2020 Jul 7.

Discipline of Pathology, School of Medical Sciences and Bosch Institute, Charles Perkins Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, 2006, Australia.

Colorectal cancer (CRC) is still a big killer nowadays, but the precise underlying mechanism remains to be explored. It is believed that imbalance of host immunity in the local microenvironment plays a critical role in the tumorigenesis of CRC. IL-34 is inversely correlated with overall survival in CRC patients, perhaps via regulating terminal differentiation of a subset of macrophages (M2). Read More

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http://dx.doi.org/10.1007/s12551-020-00726-0DOI Listing

Visualizing the in vitro assembly of tropomyosin/actin filaments using TIRF microscopy.

Biophys Rev 2020 Jul 7. Epub 2020 Jul 7.

School of Medical Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.

Tropomyosins are elongated alpha-helical proteins that form co-polymers with most actin filaments within a cell and play important roles in the structural and functional diversification of the actin cytoskeleton. How the assembly of tropomyosins along an actin filament is regulated and the kinetics of tropomyosin association with an actin filament is yet to be fully determined. A recent series of publications have used total internal reflection fluorescence (TIRF) microscopy in combination with advanced surface and protein chemistry to visualise the molecular assembly of actin/tropomyosin filaments in vitro. Read More

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http://dx.doi.org/10.1007/s12551-020-00720-6DOI Listing

Thank you (obrigado) Cris and happy Bday (Parabéns)!

Authors:
Vasco Sequeira

Biophys Rev 2020 Jul 4. Epub 2020 Jul 4.

Comprehensive Heart Failure Center (CHFC), University Clinic Würzburg, Würzburg, Germany.

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http://dx.doi.org/10.1007/s12551-020-00712-6DOI Listing

Recollections of my Ph. D. research in Professor Cris dos Remedios' laboratory.

Biophys Rev 2020 Jun 29. Epub 2020 Jun 29.

NSW Health Pathology, Sutherland Centre of Immunology, Pathology Building, Sutherland Hospital, Kingsway, Caringbah, NSW, 2229, Australia.

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http://dx.doi.org/10.1007/s12551-020-00707-3DOI Listing

Cris dos Remedios; a Driving Force in Muscle Research.

Authors:
Pauline Bennett

Biophys Rev 2020 Jun 24. Epub 2020 Jun 24.

The Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, New Hunt's House, Guy's Campus, Kings College London, London, SE1 1UL, UK.

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http://dx.doi.org/10.1007/s12551-020-00704-6DOI Listing

A comprehensive review of tumor proliferative and suppressive role of semaphorins and therapeutic approaches.

Biophys Rev 2020 Jun 23. Epub 2020 Jun 23.

Department of Biochemistry and Microbiology, North South University, Dhaka, 1229, Bangladesh.

Semaphorins have been traditionally known as axon guidance proteins that negatively regulate axonal growth. However, in the past couple of decades, their versatile role in so many other biological processes has come to prominence as well. One such example is their role in cancer. Read More

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http://dx.doi.org/10.1007/s12551-020-00709-1DOI Listing

Toward understanding of evolutionary constraints: experimental and theoretical approaches.

Biophys Rev 2020 Jun 22. Epub 2020 Jun 22.

Universal Biology Institute, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.

Although organisms have diversified remarkably through evolution, they do not exhibit unlimited variability. During evolution, the phenotypic changes do not occur at random; instead, they are directional and restricted by the constraints imposed on them. Despite the perceived importance of characterizing the unevenness of these changes, studies on evolutionary constraints have been primarily qualitative in nature. Read More

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http://dx.doi.org/10.1007/s12551-020-00708-2DOI Listing

Early adjustments in mitochondrial structure and function in skeletal muscle to high altitude: design and rationale of the first study from the Kilimanjaro Biobank.

Authors:
G J M Stienen

Biophys Rev 2020 Jun 22. Epub 2020 Jun 22.

Department of Physiology, Kilimanjaro Christian Medical University College, PO Box 2240, Moshi, Tanzania.

The physiological acclimatisation and adaptation processes in skeletal muscle at high altitude are of high medical and social relevance not only to understand limitations in physical performance at high altitude but also to understand the consequences of hypoxemia and tissue hypoxia in critically ill patients. Of particular importance in these processes are the alterations in content and function of mitochondria and myoglobin. The majority of studies on oxygen delivery to the tissues and utilisation by the cellular metabolism at high altitude were performed after prolonged stay at high altitude and in altitude-adapted highlanders. Read More

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http://dx.doi.org/10.1007/s12551-020-00710-8DOI Listing

Prof. Cristobal dos Remedios and the Sydney Heart Bank: enabling translatable heart failure research.

Biophys Rev 2020 Jun 22. Epub 2020 Jun 22.

Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, 2109 Adelbert Rd, Robbins E522, Cleveland, OH, 44106, USA.

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http://dx.doi.org/10.1007/s12551-020-00711-7DOI Listing

Research exchange with Cris: from fluorescence spectroscopy to human myocardium.

Biophys Rev 2020 Jun 21. Epub 2020 Jun 21.

Department of Physics, Faculty of Science and Engineering, Waseda University, Tokyo, Japan.

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http://dx.doi.org/10.1007/s12551-020-00706-4DOI Listing

NMR techniques in studying water in biotechnological systems.

Authors:
Victor V Rodin

Biophys Rev 2020 Jun 15;12(3):683-701. Epub 2020 Jun 15.

Institute of Organic Chemistry, Johannes Kepler University Linz, Altenbergerstraße 69, 4040, Linz, Austria.

Different NMR methodologies have been considered in studying water as a part of the structure of heterogeneous biosystems. The current work mostly describes NMR techniques to investigate slow translational dynamics of molecules affecting anisotropic properties of polymers and biomaterials. With these approaches, information about organized structures and their stability could be obtained in conditions when external factors affect biomolecules. Read More

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http://dx.doi.org/10.1007/s12551-020-00694-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7311624PMC

Studies on the impellers generating force in muscle.

Authors:
Toshio Ando

Biophys Rev 2020 Jun 11. Epub 2020 Jun 11.

Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan.

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http://dx.doi.org/10.1007/s12551-020-00705-5DOI Listing

The Sydney Heart Bank: a core facility that goes the extra mile to advance cardiac research.

Authors:
Sabine van Dijk

Biophys Rev 2020 Jun 10. Epub 2020 Jun 10.

Department of Pharmacology, University of California, Davis, Davis, CA, USA.

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http://dx.doi.org/10.1007/s12551-020-00703-7DOI Listing

Biophysical Reviews-Quantitative analysis of biological phenomenon.

Authors:
Damien Hall

Biophys Rev 2020 Jun 4;12(3):601-605. Epub 2020 Jun 4.

Department of Life Sciences and Applied Chemistry, Nagoya Institute of Technology, Gokiso Showa, Nagoya, Aichi, 466-8555, Japan.

This Editorial first describes the articles constituting the current Issue (Volume 12 Issue 3). It then goes on to outline the formal invitation procedure for those interested in submitting a review article to the journal. The Editorial concludes by describing the nomination process for the 2021 Michèle Auger Award for Young Scientists' Independent Research. Read More

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http://dx.doi.org/10.1007/s12551-020-00702-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7272135PMC

Biophysical review's 'meet the editors series'-a profile of Naranamangalam R. Jagannathan.

Biophys Rev 2020 Jun 27;12(3):607-614. Epub 2020 May 27.

Department of Radiology, Chettinad Academy of Research & Education, Kelambakkam, TN, 603103, India.

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http://dx.doi.org/10.1007/s12551-020-00700-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7311622PMC

Recent progress and current opinions in Brillouin microscopy for life science applications.

Biophys Rev 2020 Jun 26;12(3):615-624. Epub 2020 May 26.

Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA.

Many important biological functions and processes are reflected in cell and tissue mechanical properties such as elasticity and viscosity. However, current techniques used for measuring these properties have major limitations, such as that they can often not measure inside intact cells and/or require physical contact-which cells can react to and change. Brillouin light scattering offers the ability to measure mechanical properties in a non-contact and label-free manner inside of objects with high spatial resolution using light, and hence has emerged as an attractive method during the past decade. Read More

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http://dx.doi.org/10.1007/s12551-020-00701-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7311586PMC

Biophysical nanocharacterization of liver sinusoidal endothelial cells through atomic force microscopy.

Biophys Rev 2020 Jun 18;12(3):625-636. Epub 2020 May 18.

Research Centre for Nanometer-Scale Science and Advanced Materials, NANOSAM, Faculty of Physics, Astronomy and Advanced Computer Science, Jagiellonian University, Krakow, Poland.

The structural-functional hallmark of the liver sinusoidal endothelium is the presence of fenestrae grouped in sieve plates. Fenestrae are open membrane bound pores supported by a (sub)membranous cytoskeletal lattice. Changes in number and diameter of fenestrae alter bidirectional transport between the sinusoidal blood and the hepatocytes. Read More

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http://dx.doi.org/10.1007/s12551-020-00699-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7311612PMC

RNA phase separation-mediated direction of molecular trafficking under conditions of molecular crowding.

Biophys Rev 2020 Jun 16;12(3):669-676. Epub 2020 May 16.

Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan.

Living cells are highly crowded with large and small biomolecules. The total concentration of biomolecules can reach 400 mg/ml, and 40% of the cell volume is occupied by biomolecules. Droplet formation in cells via liquid-liquid phase separation may play a role in controlling biochemical reactions in this complex molecular environment. Read More

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http://dx.doi.org/10.1007/s12551-020-00696-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7311588PMC

Biophysical characterization of dynamic structures of immunoglobulin G.

Biophys Rev 2020 Jun 15;12(3):637-645. Epub 2020 May 15.

Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan.

Immunoglobulin G (IgG) is a major antibody and functions as a hub linking specific antigen binding and recruitment of effector molecules typified by Fcγ receptors (FcγRs). These activities are associated primarily with interactions involving its Fab and Fc sites, respectively. An IgG molecule is characterized by a multiple domain modular structure with conserved N-glycosylation in Fc. Read More

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http://dx.doi.org/10.1007/s12551-020-00698-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7311591PMC

Analysis of stones formed in the human gall bladder and kidney using advanced spectroscopic techniques.

Biophys Rev 2020 Jun 14;12(3):647-668. Epub 2020 May 14.

Department of Urology and Nephrology, Opal Hospital, Kakarmatta, Varanasi, Uttar Pradesh, 221010, India.

Stone diseases (gallstones and kidney stones) are extremely painful and often cause death. The prime aim of biomedical research in this area has been determination of factors resulting in stone formation inside the gallbladder and urinary tract. Many theories have been put forward to explain the mechanism of stone formation and their growth; however, their complete cycle of pathogenesis is still under debate. Read More

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http://dx.doi.org/10.1007/s12551-020-00697-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7311631PMC

Understanding metabolic adaptation by using bacterial laboratory evolution and trans-omics analysis.

Biophys Rev 2020 Jun 11;12(3):677-682. Epub 2020 May 11.

Center for Biosystems Dynamics Research, RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan.

Many diseases such as metabolic syndrome, cancer, inflammatory diseases, and pathological phenomena can be understood as an adaptive reconstitution of the metabolic state (metabolic adaptation). One of the effective approaches to reveal the property of metabolic networks is using model organisms such as microorganisms that are easier to experiment with than higher organisms. Using the laboratory evolution approach, we can elucidate the evolutionary dynamics in various stress environments, which provide us an understanding of the metabolic adaptation. Read More

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http://dx.doi.org/10.1007/s12551-020-00695-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7311587PMC

Dominant rule of community effect in synchronized beating behavior of cardiomyocyte networks.

Authors:
Kenji Yasuda

Biophys Rev 2020 Apr 4;12(2):481-501. Epub 2020 May 4.

Department of Physics, School of Advanced Science and Engineering, Waseda University 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan.

Exploiting the combination of latest microfabrication technologies and single cell measurement technologies, we can measure the interactions of single cells, and cell networks from "algebraic" and "geometric" perspectives under the full control of their environments and interactions. However, the experimental constructive single cell-based approach still remains the limitations regarding the quality and condition control of those cells. To overcome these limitations, mathematical modeling is one of the most powerful complementary approaches. Read More

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http://dx.doi.org/10.1007/s12551-020-00688-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7242600PMC

Biophysical Reviews' national biophysical society partnership program.

Authors:
Damien Hall

Biophys Rev 2020 Apr 29;12(2):187-192. Epub 2020 Apr 29.

Laboratory of Biochemistry and Genetics, NIDDK, NIH, Bld. 8, Bethesda, MD, 20892-0830, USA.

This Special Issue is focused on the Biophysical Society of Japan. It represents the first in a series tasked with introducing an individual national biophysical society to the wider biophysical community. In this Editorial for Volume 12 Issue 2, I first outline the nature and goals of this program before going on to describe the contents of the Special Issue that relate to the activities organized by the Biophysical Society of Japan and the scope of the research performed by its members. Read More

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http://dx.doi.org/10.1007/s12551-020-00693-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7242517PMC

Biophysical research in Hokkaido University, Japan.

Biophys Rev 2020 Apr 28;12(2):233-236. Epub 2020 Apr 28.

Faculty of Advanced Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo, 060-0810, Japan.

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http://dx.doi.org/10.1007/s12551-020-00649-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7242605PMC

Opto-thermal diffusiophoresis of soft biological matter: from physical principle to molecular manipulation.

Biophys Rev 2020 Apr 17;12(2):309-315. Epub 2020 Apr 17.

Department of Physics, Kyushu University, Fukuoka, Japan.

Transport of ions and molecules under external field gradients is fundamental phenomena relevant to many biological systems including molecular motors in nature. As inspired from such biological transport, novel optical manipulation by using local solute gradient and the creation of self-propulsive particles are being developed using this technology. In this review article, we describe the basic principles behind those transport phenomena under a temperature and a solute concentration gradient and discuss novel manipulation tools for soft biological materials. Read More

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http://dx.doi.org/10.1007/s12551-020-00692-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7242552PMC

Unique phase behavior in cell size space: synergistic effect of molecular crowding and confinement.

Biophys Rev 2020 Apr 10;12(2):385-386. Epub 2020 Apr 10.

Komaba Institute for Science, The University of Tokyo, Bunkyo, Japan.

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http://dx.doi.org/10.1007/s12551-020-00656-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7242570PMC

Theoretical identification of thermostabilizing amino acid mutations for G-protein-coupled receptors.

Biophys Rev 2020 Apr 8;12(2):323-332. Epub 2020 Apr 8.

Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan.

Thermostabilization of a membrane proteins, especially G-protein-coupled receptors (GPCRs), is often necessary for biochemical applications and pharmaceutical studies involving structure-based drug design. Here we review our theoretical, physics-based method for identifying thermostabilizing amino acid mutations. Its novel aspects are the following: The entropic effect originating from the translational displacement of hydrocarbon groups within the lipid bilayer is treated as a pivotal factor; a reliable measure of thermostability is introduced and a mutation which enlarges the measure to a significant extent is chosen; and all the possible mutations can be examined with moderate computational effort. Read More

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http://dx.doi.org/10.1007/s12551-020-00678-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7242571PMC

Correlation between the numbers of rotation steps in the ATPase and proton-conducting domains of F- and V-ATPases.

Biophys Rev 2020 Apr 8;12(2):303-307. Epub 2020 Apr 8.

Applied Chemistry, Graduate School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan.

This letter reports the correlation in the number of distinct rotation steps between the F/V and F/V domains that constitute common rotary F- and V-ATP synthases/ATPases. Recent single-molecule studies on the F-ATPase revealed differences in the number of discrete steps in rotary catalysis between different organisms-6 steps per turn in bacterial types and mitochondrial F from yeast, and 9 steps in the mammalian mitochondrial F domains. The number of rotational steps that F domain makes is thought to correspond to that of proteolipid subunits within the rotating c-ring present in F. Read More

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http://dx.doi.org/10.1007/s12551-020-00668-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7242557PMC

Microfluidic approaches for the analysis of protein-protein interactions in solution.

Biophys Rev 2020 Apr 8;12(2):575-585. Epub 2020 Apr 8.

Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.

Exploration and characterisation of the human proteome is a key objective enabling a heightened understanding of biological function, malfunction and pharmaceutical design. Since proteins typically exhibit their behaviour by binding to other proteins, the challenge of probing protein-protein interactions has been the focus of new and improved experimental approaches. Here, we review recently developed microfluidic techniques for the study and quantification of protein-protein interactions. Read More

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http://dx.doi.org/10.1007/s12551-020-00679-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7242286PMC

Current status and issues of protein solution biophysics-Session 1SDP.

Biophys Rev 2020 Apr 4;12(2):263-264. Epub 2020 Apr 4.

Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Tokyo, Japan.

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http://dx.doi.org/10.1007/s12551-020-00671-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7242577PMC

Overview of Taiwan-Japan joint symposium (2SDP) on structural biology using X-ray crystallography and cryo-EM at the 2019 BSJ meeting.

Authors:
Takeshi Murata

Biophys Rev 2020 Apr 27;12(2):275-276. Epub 2020 Mar 27.

Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba, 263-8522, Japan.

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http://dx.doi.org/10.1007/s12551-020-00666-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7100510PMC

Role of atomic contacts in vibrational energy transfer in myoglobin.

Biophys Rev 2020 Apr 23;12(2):511-518. Epub 2020 Mar 23.

Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan.

Heme proteins are ideal systems to investigate vibrational energy flow at the atomic level. Upon photoexcitation, a large amount of excess vibrational energy is selectively deposited on heme due to extremely fast internal conversion. This excess energy is redistributed to the surrounding protein moiety and then to water. Read More

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http://dx.doi.org/10.1007/s12551-020-00681-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7242529PMC

Heterogeneous fluid-like movements of chromatin and their implications to transcription.

Biophys Rev 2020 Apr 23;12(2):461-468. Epub 2020 Mar 23.

Department of Applied Physics, Nagoya University, Nagoya, 464-8603, Japan.

Eukaryotic chromatin is a complex of genome DNA and associated proteins, and its structure and dynamics play a crucial role in regulating DNA functions. Chromatin takes rather irregular structures in the nucleus and exhibits heterogeneous sub-diffusive movements as polymers fluctuating in a fluid state. Using genome-wide single-nucleosome tracking data, heterogeneity of movements was statistically analyzed, which categorized chromatin into two types: slow chromatin that moves under structurally constrained environments and fast chromatin that moves with less constraints. Read More

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http://dx.doi.org/10.1007/s12551-020-00675-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7242551PMC

Allosteric communication in molecular machines via information exchange: what can be learned from dynamical modeling.

Biophys Rev 2020 Apr 20;12(2):443-452. Epub 2020 Mar 20.

Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, 920-1192, Japan.

Allosteric regulation is crucial for the operation of protein machines and molecular motors. A major challenge is to characterize and quantify the information exchange underlying allosteric communication between remote functional sites in a protein, and to identify the involved relevant pathways. We review applications of two topical approaches of dynamical protein modeling, a kinetic-based single-molecule stochastic model, which employs information thermodynamics to quantify allosteric interactions, and structure-based coarse-grained modeling to characterize intra-molecular couplings in terms of conformational motions and propagating mechanical strain. Read More

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http://dx.doi.org/10.1007/s12551-020-00667-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7242553PMC

Biological phase separation: cell biology meets biophysics.

Biophys Rev 2020 Apr 18;12(2):519-539. Epub 2020 Mar 18.

Department of Future Basic Medicine, Nara Medical University, Kashihara, Nara, Japan.

Progress in development of biophysical analytic approaches has recently crossed paths with macromolecule condensates in cells. These cell condensates, typically termed liquid-like droplets, are formed by liquid-liquid phase separation (LLPS). More and more cell biologists now recognize that many of the membrane-less organelles observed in cells are formed by LLPS caused by interactions between proteins and nucleic acids. Read More

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http://dx.doi.org/10.1007/s12551-020-00680-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7242575PMC

Accurate and rapid calculation of hydration free energy and its physical implication for biomolecular functions.

Biophys Rev 2020 Apr 17;12(2):469-480. Epub 2020 Mar 17.

Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan.

Here we review a new method for calculating a hydration free energy (HFE) of a solute and discuss its physical implication for biomolecular functions in aqueous environments. The solute hydration is decomposed into processes 1 and 2. A cavity matching the geometric characteristics of the solute at the atomic level is created in process 1. Read More

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http://dx.doi.org/10.1007/s12551-020-00686-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7242554PMC

Methods and application of coherent X-ray diffraction imaging of noncrystalline particles.

Biophys Rev 2020 Apr 16;12(2):541-567. Epub 2020 Mar 16.

RIKEN SPring-8 Center, 1-1-1 Kohto, Sayo, Sayo-gun, Hyogo, 679-5148, Japan.

Microscopic imaging techniques have been developed to visualize events occurring in biological cells. Coherent X-ray diffraction imaging is one of the techniques applicable to structural analyses of cells and organelles, which have never been crystallized. In the experiment, a single noncrystalline particle is illuminated by an X-ray beam with almost complete spatial coherence. Read More

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http://dx.doi.org/10.1007/s12551-020-00690-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7242594PMC