510 results match your criteria Biophysical reviews[Journal]


Membrane biophysics session.

Biophys Rev 2019 Apr 2. Epub 2019 Apr 2.

School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne, VIC, 3010, Australia.

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http://dx.doi.org/10.1007/s12551-019-00515-4DOI Listing
April 2019
1 Read

ABA/ASB Membrane Biophysics session II 2018.

Biophys Rev 2019 Mar 21. Epub 2019 Mar 21.

School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia.

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http://dx.doi.org/10.1007/s12551-019-00516-3DOI Listing

Unified theoretical description of the kinetics of protein aggregation.

Biophys Rev 2019 Apr 19;11(2):191-208. Epub 2019 Mar 19.

Institute for Protein Research, Osaka University, 3-1- Yamada-oka, Suita, Osaka, 565-0871, Japan.

Solution conditions chosen for the production of amyloid can also promote formation of significant extents of amorphous protein aggregate. In one interpretation, the amyloid and amorphous aggregation pathways are considered to be in competition with each other. An alternative conceptualization involves considering amorphous aggregation as an obligatory intermediate process of the amyloid formation pathway. Read More

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http://dx.doi.org/10.1007/s12551-019-00506-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6441446PMC
April 2019
1 Read

Ionic liquids and protein folding-old tricks for new solvents.

Biophys Rev 2019 Apr 19;11(2):209-225. Epub 2019 Mar 19.

Institute for Protein Research, Osaka University, 3-1-Yamada-oka, Suita, Osaka, 565-0871, Japan.

One important aspect of the green chemistry revolution has been the use of ionic liquids as the solvent in liquid-phase enzymatic catalysis. An essential requirement for protein enzyme function is the correct folding of the polypeptide chain into its functional "native" state. Quantitative assessment of protein structure may be carried out either empirically, or by using model-based characterization procedures, in which the parameters are defined in terms of a standard reference state. Read More

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http://dx.doi.org/10.1007/s12551-019-00509-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6441443PMC

Numerical study of hydromagnetic axisymmetric peristaltic flow at high Reynolds number and wave number.

Biophys Rev 2019 Apr 12;11(2):139-147. Epub 2019 Mar 12.

Department of Mathematics and Statistics, International Islamic University Islamabad, Islamabad, 44000, Pakistan.

The computational study of MHD peristaltic motion is investigated for axisymmetric flow problem. The developed model is present in the form of partial differential equations. Then obtained partial differential equations are transferred into stream-vorticity (ψ - ω) form. Read More

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http://dx.doi.org/10.1007/s12551-019-00511-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6441442PMC

Advances in domain and subunit localization technology for electron microscopy.

Biophys Rev 2019 Apr 5;11(2):149-155. Epub 2019 Mar 5.

Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Osaka, Japan.

The award of the 2017 Nobel Prize in chemistry, 'for developing cryo-electron microscopy for the high-resolution structure determination of biomolecules in solution', was recognition that this method, and electron microscopy more generally, represent powerful techniques in the scientific armamentarium for atomic level structural assessment. Technical advances in equipment, software, and sample preparation, have allowed for high-resolution structural determination of a range of complex biological machinery such that the position of individual atoms within these mega-structures can be determined. However, not all targets are amenable to attaining such high-resolution structures and some may only be resolved at so-called intermediate resolutions. Read More

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http://dx.doi.org/10.1007/s12551-019-00513-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6441409PMC
April 2019
10 Reads

Chara braunii genome: a new resource for plant electrophysiology.

Authors:
M J Beilby

Biophys Rev 2019 Apr 4;11(2):235-239. Epub 2019 Mar 4.

School of Physics, University of NSW, Kensington, NSW, 2052, Australia.

The large-celled green alga Chara provided early electrophysiological data, but this model organism lost popularity once the smaller cells of higher plants became accessible to electrophysiology and genetic manipulation. However, with the sequencing of the Chara braunii genome (Nishiyama et al. Cell 174: 448-464, 2018), the molecular identity of the underlaying ion transporters in Characeae can be found and placed in evolutionary context. Read More

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http://dx.doi.org/10.1007/s12551-019-00512-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6441437PMC

Letter from the Editor.

Biophys Rev 2019 Apr 4;11(2):127-128. Epub 2019 Mar 4.

The University of Sydney, Sydney, Australia.

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http://dx.doi.org/10.1007/s12551-019-00510-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6441410PMC

Recollections of 50 years of research in biophysics: a matter of hard work and luck.

Biophys Rev 2019 Apr 27;11(2):135-137. Epub 2019 Feb 27.

Discipline of Anatomy & Histology, Faculty of Medicine and Heath, The University of Sydney, Sydney, 2006, Australia.

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http://dx.doi.org/10.1007/s12551-019-00502-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6441438PMC

Photoreaction pathways and photointermediates of retinal-binding photoreceptor proteins as revealed by in situ photoirradiation solid-state NMR spectroscopy.

Biophys Rev 2019 Apr 27;11(2):167-181. Epub 2019 Feb 27.

Graduate School of Engineering, Yokohama National University, Yokohama, 240-8501, Japan.

Photoirradiation solid-state NMR spectroscopy is a powerful means to study photoreceptor retinal-binding proteins by the detection of short-lived photointermediates to elucidate the photoreaction cycle and photoactivated structural changes. An in situ photoirradiation solid-state NMR apparatus has been developed for the irradiation of samples with extremely high efficiency to enable observation of photointermediates which are stationary trapped states. Such observation enables elucidation of the photoreaction processes of photoreceptor membrane proteins. Read More

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http://dx.doi.org/10.1007/s12551-019-00501-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6441423PMC

Trials and tribulations of an early career academic pathway after returning to Australia: reflections from an early career investigator.

Authors:
Amy Li

Biophys Rev 2019 Apr 27;11(2):131-134. Epub 2019 Feb 27.

Discipline of Anatomy & Histology, University of Sydney, Sydney, 2006, Australia.

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http://dx.doi.org/10.1007/s12551-019-00507-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6441415PMC

Proteases from dengue, West Nile and Zika viruses as drug targets.

Biophys Rev 2019 Apr 26;11(2):157-165. Epub 2019 Feb 26.

Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia.

Proteases from flaviviruses have gained substantial interest as potential drug targets to combat infectious diseases caused by dengue, West Nile, Zika and related viruses. Despite nearly two decades of drug discovery campaigns, promising lead compounds for clinical trials have not yet been identified. The main challenges for successful lead compound development are associated with limited drug-likeness of inhibitors and structural ambiguity of the protease target. Read More

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http://dx.doi.org/10.1007/s12551-019-00508-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6441445PMC

A perspective on the diagnostics, prognostics, and therapeutics of microRNAs of triple-negative breast cancer.

Biophys Rev 2019 Apr 22;11(2):227-234. Epub 2019 Feb 22.

Cancer biology laboratory, Department of Biochemistry and Bioinformatics, GIS, GITAM (Deemed to be University), Visakhapatnam, Andhra Pradesh, 530045, India.

Triple-negative breast cancer (TNBC) is the most aggressive and prevalent subtype of breast cancer in women worldwide. Currently, chemotherapy remains the main modality for the treatment at an early stage, as there is no approved targeted therapy for early TNBC. In this review, we investigate the use of microRNAs (miRNAs), which play a key role in the post-transcriptional regulation of genes involved in the key biological processes, namely proliferation, differentiation, angiogenesis, migration, apoptosis, and carcinogenesis. Read More

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http://dx.doi.org/10.1007/s12551-019-00503-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6441430PMC
April 2019
1 Read

A note of appreciation for Prof. Cristobal dos Remedios on behalf of Biophysical Reviews.

Authors:
Damien Hall

Biophys Rev 2019 Apr 19;11(2):129-130. Epub 2019 Feb 19.

Laboratory for Multiscale Structural Biology, Institute for Protein Research, Osaka University, 3-1-Yamadaoka, Suita, Osaka, 565-0871, Japan.

Following the initial five-year tenure (2009-2014) of the founding Chief Editor, Dr. Jean Garnier, Prof. Cristobal dos Remedios (University of Sydney) assumed responsibility for Biophysical Reviews as the second Chief Editor (2014-2019). Read More

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http://dx.doi.org/10.1007/s12551-019-00505-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6441412PMC

Mathematical models applied to thyroid cancer.

Biophys Rev 2019 Apr 15;11(2):183-189. Epub 2019 Feb 15.

Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, 18618-689, Brazil.

Thyroid cancer is the most prevalent endocrine neoplasia in the world. The use of mathematical models on the development of tumors has yielded numerous results in this field and modeling with differential equations is present in many papers on cancer. In order to know the use of mathematical models with differential equations or similar in the study of thyroid cancer, studies since 2006 to date was reviewed. Read More

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http://dx.doi.org/10.1007/s12551-019-00504-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6441425PMC
April 2019
1 Read

Bayesian statistical learning for big data biology.

Biophys Rev 2019 Feb 7;11(1):95-102. Epub 2019 Feb 7.

Department of Statistics, University of British Columbia, Vancouver, Canada.

Bayesian statistical learning provides a coherent probabilistic framework for modelling uncertainty in systems. This review describes the theoretical foundations underlying Bayesian statistics and outlines the computational frameworks for implementing Bayesian inference in practice. We then describe the use of Bayesian learning in single-cell biology for the analysis of high-dimensional, large data sets. Read More

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http://dx.doi.org/10.1007/s12551-019-00499-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6381359PMC
February 2019

Stems cells, big data and compendium-based analyses for identifying cell types, signalling pathways and gene regulatory networks.

Biophys Rev 2019 Feb 25;11(1):41-50. Epub 2019 Jan 25.

School of Medicine, Western Sydney University, Campbelltown, NSW, Australia.

Identification of new drug and cell therapy targets for disease treatment will be facilitated by a detailed molecular understanding of normal and disease development. Human pluripotent stem cells can provide a large in vitro source of human cell types and, in a growing number of instances, also three-dimensional multicellular tissues called organoids. The application of stem cell technology to discovery and development of new therapies will be aided by detailed molecular characterisation of cell identity, cell signalling pathways and target gene networks. Read More

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http://dx.doi.org/10.1007/s12551-018-0486-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6381357PMC
February 2019
1 Read

Big data challenges in genome informatics.

Authors:
Ka-Chun Wong

Biophys Rev 2019 Feb 25;11(1):51-54. Epub 2019 Jan 25.

City University of Hong Kong, Kowloon, Hong Kong.

In recent years, we have witnessed a big data explosion in genomics, thanks to the improvement in high-throughput technologies at drastically decreasing costs. We are entering the era of millions of available genomes. Notably, each genome can be composed of billions of nucleotides stored as plain text files in gigabytes (GBs). Read More

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http://dx.doi.org/10.1007/s12551-018-0493-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6381353PMC
February 2019

Big data: the elements of good questions, open data, and powerful software.

Biophys Rev 2019 Feb 25;11(1):1-3. Epub 2019 Jan 25.

Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia.

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http://dx.doi.org/10.1007/s12551-019-00500-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6381355PMC
February 2019

Host and microbiome multi-omics integration: applications and methodologies.

Biophys Rev 2019 Feb 9;11(1):55-65. Epub 2019 Jan 9.

State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, No.79 Qingchun Road, Hangzhou, 310003, Zhejiang, China.

The study of the microbial community-the microbiome-associated with a human host is a maturing research field. It is increasingly clear that the composition of the human's microbiome is associated with various diseases such as gastrointestinal diseases, liver diseases and metabolic diseases. Using high-throughput technologies such as next-generation sequencing and mass spectrometry-based metabolomics, we are able to comprehensively sequence the microbiome-the metagenome-and associate these data with the genomic, epigenomics, transcriptomic and metabolic profile of the host. Read More

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http://link.springer.com/10.1007/s12551-018-0491-7
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http://dx.doi.org/10.1007/s12551-018-0491-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6381360PMC
February 2019
12 Reads

A review of big data applications of physiological signal data.

Biophys Rev 2019 Feb 9;11(1):83-87. Epub 2019 Jan 9.

Oxygen Research Ltd, 8 Vassileos Constantinou Street, 3075, Limassol, Cyprus.

The proliferation of smart physiological signal monitoring sensors, combined with the advancement of telemetry and intelligent communication systems, has led to an explosion in healthcare data in the past few years. Additionally, access to cheaper and more effective power and storage mechanisms has significantly increased the availability of healthcare data for the development of big data applications. Big data applications in healthcare are concerned with the analysis of datasets which are too big, too fast, and too complex for healthcare providers to process and interpret with existing tools. Read More

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http://dx.doi.org/10.1007/s12551-018-0495-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6381367PMC
February 2019

RNA polymerase II ChIP-seq-a powerful and highly affordable method for studying fungal genomics and physiology.

Biophys Rev 2019 Feb 9;11(1):79-82. Epub 2019 Jan 9.

Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau SAR, China.

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http://dx.doi.org/10.1007/s12551-018-00497-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6381363PMC
February 2019

The rise of the distributions: why non-normality is important for understanding the transcriptome and beyond.

Authors:
Jessica C Mar

Biophys Rev 2019 Feb 7;11(1):89-94. Epub 2019 Jan 7.

Australian Institute for Bioengineering and Nanotechnology, University of Queensland, QLD, Brisbane, 4072, Australia.

The application of statistics has been instrumental in clarifying our understanding of the genome. While insights have been derived for almost all levels of genome function, most importantly, statistics has had the greatest impact on improving our knowledge of transcriptional regulation. But the drive to extract the most meaningful inferences from big data can often force us to overlook the fundamental role that statistics plays, and specifically, the basic assumptions that we make about big data. Read More

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http://dx.doi.org/10.1007/s12551-018-0494-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6381358PMC
February 2019
2 Reads

Precision medicine review: rare driver mutations and their biophysical classification.

Biophys Rev 2019 Feb 4;11(1):5-19. Epub 2019 Jan 4.

Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44106, USA.

How can biophysical principles help precision medicine identify rare driver mutations? A major tenet of pragmatic approaches to precision oncology and pharmacology is that driver mutations are very frequent. However, frequency is a statistical attribute, not a mechanistic one. Rare mutations can also act through the same mechanism, and as we discuss below, "latent driver" mutations may also follow the same route, with "helper" mutations. Read More

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http://link.springer.com/10.1007/s12551-018-0496-2
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http://dx.doi.org/10.1007/s12551-018-0496-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6381362PMC
February 2019
17 Reads

Mining data and metadata from the gene expression omnibus.

Biophys Rev 2019 Feb 29;11(1):103-110. Epub 2018 Dec 29.

BD2K-LINCS Data Coordination and Integration Center; Knowledge Management Center for the Illuminating the Druggable Genome; Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, Box 1603, One Gustave L. Levy Place, New York, NY, 10029, USA.

Publicly available gene expression datasets deposited in the Gene Expression Omnibus (GEO) are growing at an accelerating rate. Such datasets hold great value for knowledge discovery, particularly when integrated. Although numerous software platforms and tools have been developed to enable reanalysis and integration of individual, or groups, of GEO datasets, large-scale reuse of those datasets is impeded by minimal requirements for standardized metadata both at the study and sample levels as well as uniform processing of the data across studies. Read More

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http://dx.doi.org/10.1007/s12551-018-0490-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6381352PMC
February 2019
2 Reads

Hi-C analysis: from data generation to integration.

Biophys Rev 2019 Feb 20;11(1):67-78. Epub 2018 Dec 20.

IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy.

In the epigenetics field, large-scale functional genomics datasets of ever-increasing size and complexity have been produced using experimental techniques based on high-throughput sequencing. In particular, the study of the 3D organization of chromatin has raised increasing interest, thanks to the development of advanced experimental techniques. In this context, Hi-C has been widely adopted as a high-throughput method to measure pairwise contacts between virtually any pair of genomic loci, thus yielding unprecedented challenges for analyzing and handling the resulting complex datasets. Read More

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http://dx.doi.org/10.1007/s12551-018-0489-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6381366PMC
February 2019

Towards testing big data analytics software: the essential role of metamorphic testing.

Biophys Rev 2019 Feb 18;11(1):123-125. Epub 2018 Dec 18.

School of Computer Science, Wuhan University, Wuhan, China.

In the rapidly growing field of big data analysis, scientists from numerous domains such as computer science and biology are constantly challenged by an unprecedented amount of data. While many software programs have been constructed to support processing and analyzing continuous information flow, one under-appreciated challenge in this field is software quality assurance of these big data software platforms. Metamorphic testing, which was proposed to alleviate the oracle problem in the software engineering community, has become an effective approach for software verification and validation. Read More

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http://dx.doi.org/10.1007/s12551-018-0492-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6381365PMC
February 2019

Tom Pollard, father of life science policy advocacy.

Authors:
Kevin Wilson

Biophys Rev 2018 Dec 3;10(6):1499-1502. Epub 2018 Dec 3.

American Society for Cell Biology, Bethesda, MD, USA.

Tom Pollard has played an instrumental role in the creation of the life science policy and advocacy programs familiar to life scientists today. This article reviews the creation of that program and the role Tom played. In addition, it briefly discusses advocacy activities now available to life scientists and why they should participate in these activities. Read More

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http://link.springer.com/10.1007/s12551-018-0488-2
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http://dx.doi.org/10.1007/s12551-018-0488-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297092PMC
December 2018
1 Read

Opening remarks from the Editors.

Biophys Rev 2018 Dec;10(6):1479-1480

Pennsylvania Muscle Institute and Department of Physiology, University of Pennsylvania, Philadelphia, PA, USA.

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http://dx.doi.org/10.1007/s12551-018-0487-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297087PMC
December 2018
11 Reads

From solution to surface to filament: actin flux into branched networks.

Biophys Rev 2018 Dec 23;10(6):1537-1551. Epub 2018 Nov 23.

Department of Bioengineering, University of California, Berkeley, CA, USA.

The actin cytoskeleton comprises a set of filament networks that perform essential functions in eukaryotic cells. The idea that actin filaments incorporate monomers directly from solution forms both the "textbook picture" of filament elongation and a conventional starting point for quantitative modeling of cellular actin dynamics. Recent work, however, reveals that filaments created by two major regulators, the formins and the Arp2/3 complex, incorporate monomers delivered by nearby proteins. Read More

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http://dx.doi.org/10.1007/s12551-018-0469-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297094PMC
December 2018
6 Reads

Polymerization and depolymerization of actin with nucleotide states at filament ends.

Biophys Rev 2018 Dec 20;10(6):1513-1519. Epub 2018 Nov 20.

Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.

Polymerization induces hydrolysis of ATP bound to actin, followed by γ-phosphate release, which helps advance the disassembly of actin filaments into ADP-G-actin. Mechanical understanding of this correlation between actin assembly and ATP hydrolysis has been an object of intensive studies in biochemistry and structural biology for many decades. Although actin polymerization and depolymerization occur only at either the barbed or pointed ends and the kinetic and equilibrium properties are substantially different from each other, characterizing their properties is difficult to do by bulk assays, as these assays report the average of all actin filaments in solution and are therefore not able to discern the properties of individual actin filaments. Read More

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http://dx.doi.org/10.1007/s12551-018-0483-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297080PMC
December 2018
15 Reads

Mechanisms of contractile ring tension production and constriction.

Biophys Rev 2018 Dec 19;10(6):1667-1681. Epub 2018 Nov 19.

Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA.

The contractile ring is a remarkable tension-generating cellular machine that constricts and divides cells into two during cytokinesis, the final stage of the cell cycle. Since the ring's discovery, the parallels with muscle have been emphasized. Both are contractile actomyosin machineries, and long ago, a muscle-like sliding filament mechanism was proposed for the ring. Read More

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http://dx.doi.org/10.1007/s12551-018-0476-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297097PMC
December 2018
1 Read

BAR domain proteins-a linkage between cellular membranes, signaling pathways, and the actin cytoskeleton.

Biophys Rev 2018 Dec 19;10(6):1587-1604. Epub 2018 Nov 19.

Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.

Actin filament assembly typically occurs in association with cellular membranes. A large number of proteins sit at the interface between actin networks and membranes, playing diverse roles such as initiation of actin polymerization, modulation of membrane curvature, and signaling. Bin/Amphiphysin/Rvs (BAR) domain proteins have been implicated in all of these functions. Read More

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http://dx.doi.org/10.1007/s12551-018-0467-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297083PMC
December 2018
16 Reads

Molecular mechanisms of contractile-ring constriction and membrane trafficking in cytokinesis.

Biophys Rev 2018 Dec 17;10(6):1649-1666. Epub 2018 Nov 17.

Department of Molecular Genetics, Columbus, OH, USA.

In this review, we discuss the molecular mechanisms of cytokinesis from plants to humans, with a focus on contribution of membrane trafficking to cytokinesis. Selection of the division site in fungi, metazoans, and plants is reviewed, as well as the assembly and constriction of a contractile ring in fungi and metazoans. We also provide an introduction to exocytosis and endocytosis, and discuss how they contribute to successful cytokinesis in eukaryotic cells. Read More

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http://link.springer.com/10.1007/s12551-018-0479-3
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http://dx.doi.org/10.1007/s12551-018-0479-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297088PMC
December 2018
22 Reads

Building the contractile ring from the ground up: a lesson in perseverance and scientific creativity.

Biophys Rev 2018 Dec 17;10(6):1491-1497. Epub 2018 Nov 17.

Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 1051 William Moore Drive, Office: RB 254, Raleigh, NC, 27606, USA.

This contribution to the Festschrift for Professor Thomas (Tom) D. Pollard focuses on his work on the elucidation of the protein organization within the cytokinetic nodes, protein assemblies, precursors to the contractile ring. In particular, this work highlights recent discoveries in the molecular organization of the proteins that make the contractile machine in fission yeast using advanced microscopy techniques. Read More

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http://dx.doi.org/10.1007/s12551-018-0482-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297081PMC
December 2018

Does self-organized criticality drive leading edge protrusion?

Biophys Rev 2018 Dec 17;10(6):1571-1575. Epub 2018 Nov 17.

Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA.

Arp2/3 complex nucleates dendritic actin networks and plays a pivotal role in the formation of lamellipodia at the leading edge of motile cells. Mouse fibroblasts lacking functional Arp2/3 complex have the characteristic smooth, veil-like lamellipodial leading edge of wild-type cells replaced by a massive, bifurcating filopodia-like protrusions (FLPs) with fractal geometry. The nanometer-scale actin-network organization of these FLPs can be linked to the fractal geometry of the cell boundary by a self-organized criticality through the bifurcation behavior of cross-linked actin bundles. Read More

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http://link.springer.com/10.1007/s12551-018-0484-6
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http://dx.doi.org/10.1007/s12551-018-0484-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297079PMC
December 2018
11 Reads

Discovery of myosin I and Pollard-san.

Authors:
Fumio Oosawa

Biophys Rev 2018 Dec 16;10(6):1481-1482. Epub 2018 Nov 16.

Department of Physics, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan.

In this short review, I describe a brief history of the discovery of myosin I isolated from Acanthamoeba in 1973 by Tom Pollard and Ed Korn. Today, myosins form a large "family tree" that includes more than 30 types of myosins. I discuss the importance of the relationship among actin, myosin, and other actin-binding proteins, many of which were pioneered by Pollard-san ("-san" is a Japanese honorific suffix showing respect, politeness and friendship). Read More

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http://dx.doi.org/10.1007/s12551-018-0485-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297091PMC
December 2018

Multifunctional roles of tropomodulin-3 in regulating actin dynamics.

Biophys Rev 2018 Dec 14;10(6):1605-1615. Epub 2018 Nov 14.

Department of Molecular Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA.

Tropomodulins (Tmods) are proteins that cap the slow-growing (pointed) ends of actin filaments (F-actin). The basis for our current understanding of Tmod function comes from studies in cells with relatively stable and highly organized F-actin networks, leading to the view that Tmod capping functions principally to preserve F-actin stability. However, not only is Tmod capping dynamic, but it also can play major roles in regulating diverse cellular processes involving F-actin remodeling. Read More

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http://link.springer.com/10.1007/s12551-018-0481-9
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http://dx.doi.org/10.1007/s12551-018-0481-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297098PMC
December 2018
15 Reads

Building a dendritic actin filament network branch by branch: models of filament orientation pattern and force generation in lamellipodia.

Biophys Rev 2018 Dec 12;10(6):1577-1585. Epub 2018 Nov 12.

Department of Physics, Lehigh University, 16 Memorial Drive East, Bethlehem, PA, 18105, USA.

We review mathematical and computational models of the structure, dynamics, and force generation properties of dendritic actin networks. These models have been motivated by the dendritic nucleation model, which provided a mechanistic picture of how the actin cytoskeleton system powers cell motility. We describe how they aimed to explain the self-organization of the branched network into a bimodal distribution of filament orientations peaked at 35° and - 35° with respect to the direction of membrane protrusion, as well as other patterns. Read More

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http://dx.doi.org/10.1007/s12551-018-0475-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297084PMC
December 2018

"Essentially, all models are wrong, but some are useful"-a cross-disciplinary agenda for building useful models in cell biology and biophysics.

Authors:
Julien Berro

Biophys Rev 2018 Dec 12;10(6):1637-1647. Epub 2018 Nov 12.

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.

Intuition alone often fails to decipher the mechanisms underlying the experimental data in Cell Biology and Biophysics, and mathematical modeling has become a critical tool in these fields. However, mathematical modeling is not as widespread as it could be, because experimentalists and modelers often have difficulties communicating with each other, and are not always on the same page about what a model can or should achieve. Here, we present a framework to develop models that increase the understanding of the mechanisms underlying one's favorite biological system. Read More

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http://link.springer.com/10.1007/s12551-018-0478-4
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http://dx.doi.org/10.1007/s12551-018-0478-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297095PMC
December 2018
6 Reads

The Pollard lab at Salk: moving the leading edge forward.

Authors:
Henry N Higgs

Biophys Rev 2018 Dec 12;10(6):1487-1490. Epub 2018 Nov 12.

Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.

This essay will review the years that the Pollard lab was at the Salk Institute in the last half of the 1990s. It was a highly productive time both in research and in training. For me personally, it shaped my career for the better in ways I am still discovering. Read More

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http://dx.doi.org/10.1007/s12551-018-0480-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297078PMC
December 2018

Contractile protein biochemistry in the Pollard Lab in Baltimore.

Biophys Rev 2018 Dec 8;10(6):1483-1485. Epub 2018 Nov 8.

Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, CB 8231, 660 South Euclid Ave., Saint Louis, MO, 63110, USA.

We describe our search for the molecular mechanisms of cell motility with personal recollections of bucket biochemistry in Tom Pollards Lab at the Johns Hopkins, circa 1980. Read More

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http://link.springer.com/10.1007/s12551-018-0477-5
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http://dx.doi.org/10.1007/s12551-018-0477-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297093PMC
December 2018
8 Reads

Tissue engineering the cancer microenvironment-challenges and opportunities.

Biophys Rev 2018 Dec 8;10(6):1695-1711. Epub 2018 Nov 8.

CRUK Beatson Institute for Cancer Research and Institute of cancer Sciences, University of Glasgow, Garscube Campus, Switchback Road, Bearsden, Glasgow, G61 1BD, UK.

Mechanosensing is increasingly recognised as important for tumour progression. Tumours become stiff and the forces that normally balance in the healthy organism break down and become imbalanced, leading to increases in migration, invasion and metastatic dissemination. Here, we review recent advances in our understanding of how extracellular matrix properties, such as stiffness, viscoelasticity and architecture control cell behaviour. Read More

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http://dx.doi.org/10.1007/s12551-018-0466-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297082PMC
December 2018
1 Read

Num1 versus NuMA: insights from two functionally homologous proteins.

Biophys Rev 2018 Dec 6;10(6):1631-1636. Epub 2018 Nov 6.

Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA.

In both animals and fungi, spindle positioning is dependent upon pulling forces generated by cortically anchored dynein. In animals, cortical anchoring is accomplished by a ternary complex containing the dynein-binding protein NuMA and its cortical attachment machinery. The same function is accomplished by Num1 in budding yeast. Read More

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http://dx.doi.org/10.1007/s12551-018-0472-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297085PMC
December 2018

Mechanisms of formin-mediated actin assembly and dynamics.

Biophys Rev 2018 Dec 3;10(6):1553-1569. Epub 2018 Nov 3.

Department of Genetics, Cell and Developmental Biology, University of Minnesota, 420 Washington Ave SE, 6-130 MCB, Minneapolis, MN, 55455, USA.

Cellular viability requires tight regulation of actin cytoskeletal dynamics. Distinct families of nucleation-promoting factors enable the rapid assembly of filament nuclei that elongate and are incorporated into diverse and specialized actin-based structures. In addition to promoting filament nucleation, the formin family of proteins directs the elongation of unbranched actin filaments. Read More

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http://link.springer.com/10.1007/s12551-018-0468-6
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http://dx.doi.org/10.1007/s12551-018-0468-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297096PMC
December 2018
1 Read

Multiscale simulation of actin filaments and actin-associated proteins.

Biophys Rev 2018 Dec 31;10(6):1521-1535. Epub 2018 Oct 31.

Department of Chemistry, Institute of Biophysical Dynamics, and James Frank Institute, University of Chicago, Chicago, IL, USA.

Actin is an important cytoskeletal protein that serves as a building block to form filament networks that span across the cell. These networks are orchestrated by a myriad of other cytoskeletal entities including the unbranched filament-forming protein formin and branched network-forming protein complex Arp2/3. Computational models have been able to provide insights into many important structural transitions that are involved in forming these networks, and into the nature of interactions essential for actin filament formation and for regulating the behavior of actin-associated proteins. Read More

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http://dx.doi.org/10.1007/s12551-018-0474-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297090PMC
December 2018

Cytoskeletal discoveries in the plant lineage using the moss Physcomitrella patens.

Biophys Rev 2018 Dec 31;10(6):1683-1693. Epub 2018 Oct 31.

Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH, 03755, USA.

Advances in cell biology have been largely driven by pioneering work in model systems, the majority of which are from one major eukaryotic lineage, the opisthokonts. However, with the explosion of genomic information in many lineages, it has become clear that eukaryotes have incredible diversity in many cellular systems, including the cytoskeleton. By identifying model systems in diverse lineages, it may be possible to begin to understand the evolutionary origins of the eukaryotic cytoskeleton. Read More

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http://link.springer.com/10.1007/s12551-018-0470-z
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http://dx.doi.org/10.1007/s12551-018-0470-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297077PMC
December 2018
12 Reads

S100 proteins as therapeutic targets.

Authors:
Anne R Bresnick

Biophys Rev 2018 Dec 31;10(6):1617-1629. Epub 2018 Oct 31.

Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA.

The human genome codes for 21 S100 protein family members, which exhibit cell- and tissue-specific expression patterns. Despite sharing a high degree of sequence and structural similarity, the S100 proteins bind a diverse range of protein targets and contribute to a broad array of intracellular and extracellular functions. Consequently, the S100 proteins regulate multiple cellular processes such as proliferation, migration and/or invasion, and differentiation, and play important roles in a variety of cancers, autoimmune diseases, and chronic inflammatory disorders. Read More

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http://link.springer.com/10.1007/s12551-018-0471-y
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http://dx.doi.org/10.1007/s12551-018-0471-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297089PMC
December 2018
14 Reads