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Biophysical Reviews

Vivek K Singh, Jitendra Sharma, Ashok K Pathak, Charles T Ghany, M A Gondal
With the advent of improved experimental techniques and enhanced precision, laser-induced breakdown spectroscopy (LIBS) offers a robust tool for probing the chemical constituents of samples of interest in biological sciences. As the interest continues to grow rapidly, the domain of study encompasses a variety of applications vis-à-vis biological species and microbes. LIBS is basically an atomic emission spectroscopy of plasma produced by the high-power pulsed laser which is tightly focused on the surface of any kinds of target materials in any phase...
October 18, 2018: Biophysical Reviews
Po-Chia Chen, Janosch Hennig
In many biomolecular interactions, changes in the assembly states and structural conformations of participants can act as a complementary reporter of binding to functional and thermodynamic assays. This structural information is captured by a number of structural biology and biophysical techniques that are viable either as primary screens in small-scale applications or as secondary screens to complement higher throughput methods. In particular, small-angle X-ray scattering (SAXS) reports the average distance distribution between all atoms after orientational averaging...
October 10, 2018: Biophysical Reviews
Jasleen Kaur Daljit Singh, Minh Tri Luu, Ali Abbas, Shelley F J Wickham
Structural DNA nanotechnology, in which Watson-Crick base pairing drives the formation of self-assembling nanostructures, has rapidly expanded in complexity and functionality since its inception in 1981. DNA nanostructures can now be made in arbitrary three-dimensional shapes and used to scaffold many other functional molecules such as proteins, metallic nanoparticles, polymers, fluorescent dyes and small molecules. In parallel, the field of dynamic DNA nanotechnology has built DNA circuits, motors and switches...
October 2, 2018: Biophysical Reviews
Ruth Nussinov, Mingzhen Zhang, Chung-Jung Tsai, Tsung-Jen Liao, David Fushman, Hyunbum Jang
Autoinhibition is an effective mechanism that guards proteins against spurious activation. Despite its ubiquity, the distinct organizations of the autoinhibited states and their release mechanisms differ. Signaling is most responsive to the cell environment only if a small shift in the equilibrium is required to switch the system from an inactive (occluded) to an active (exposed) state. Ras signaling follows this paradigm. This underscores the challenge in pharmacological intervention to exploit and enhance autoinhibited states...
September 29, 2018: Biophysical Reviews
Keiji Naruse
It has been a long time since the term mechanobiology became widely accepted, and broad research approaches, ranging from basic biology to medical research, have been conducted from the perspective of mechanobiology. Our group created the term "mechanomedicine" focusing on the field encompassing studies of the pathology and treatment of various diseases based on the knowledge obtained from mechanobiological studies and have promoted studies in this field. In the respiratory and cardiovascular systems, not only humoral factors but also physical factors such as contraction and expansion phenomena, and feedback from such phenomena to tissues and cells are important stimuli for maintaining homeostasis...
September 29, 2018: Biophysical Reviews
Stefanie S Portelli, Elizabeth N Robertson, Cassandra Malecki, Kiersten A Liddy, Brett D Hambly, Richmond W Jeremy
Genetically triggered thoracic aortic aneurysms (TAAs) account for 30% of all TAAs and can result in early morbidity and mortality in affected individuals. Epigenetic factors are now recognised to influence the phenotype of many genetically triggered conditions and have become an area of interest because of the potential for therapeutic manipulation. Major epigenetic modulators include DNA methylation, histone modification and non-coding RNA. This review examines epigenetic modulators that have been significantly associated with genetically triggered TAAs and their potential utility for translation to clinical practice...
September 28, 2018: Biophysical Reviews
Glen Dorrington, Nikola P Chmel, Stephen R Norton, Alan M Wemyss, Katherine Lloyd, D Praveen Amarasinghe, Alison Rodger
The interpretation of data from absorbance spectroscopy experiments of liposomes in flow systems is often complicated by the fact that there is currently no easy way to account for scattering artefacts. This has proved particularly problematic for linear dichroism (LD) spectroscopy, which may be used to determine binding modes of small molecules, peptides and proteins to liposomes if we can extract the absorbance signal from the combined absorbance/scattering experiment. Equations for a modified Rayleigh-Gans-Debye (RGD) approximation to the turbidity (scattering) LD spectrum are available in the literature though have not been implemented...
September 25, 2018: Biophysical Reviews
Cristobal G Dos Remedios
No abstract text is available yet for this article.
September 24, 2018: Biophysical Reviews
Harry W Rathbone, Jeffery A Davis, Katharine A Michie, Sophia C Goodchild, Neil O Robertson, Paul M G Curmi
Considerable debate surrounds the question of whether or not quantum mechanics plays a significant, non-trivial role in photosynthetic light harvesting. Many have proposed that quantum superpositions and/or quantum transport phenomena may be responsible for the efficiency and robustness of energy transport present in biological systems. The critical experimental observations comprise the observation of coherent oscillations or "quantum beats" via femtosecond laser spectroscopy, which have been observed in many different light harvesting systems...
September 22, 2018: Biophysical Reviews
Vangelis George Kanellis, Cristobal G Dos Remedios
Various human activities lead to the pollution of ground, drinking, and wastewater with toxic metals. It is well known that metal ions preferentially bind to DNA phosphate backbones or DNA nucleobases, or both. Foreman et al. (Environ Toxicol Chem 30(8):1810-1818, 2011) reported the use of a DNA-dye based assay suitable for use as a toxicity test for potable environmental water. They compared the results of this test with the responses of live-organism bioassays. The DNA-based demonstrated that the loss of SYBR Green I fluorescence dye bound to calf thymus DNA was proportional to the toxicity of the water sample...
September 18, 2018: Biophysical Reviews
Vangelis George Kanellis
Even when present in very low concentrations, certain metal ions can have significant health impacts depending on their concentration when present in drinking water. In an effort to detect and identify trace amounts of such metals, environmental monitoring has created a demand for new and improved methods that have ever-increasing sensitivities and selectivity. This paper reviews the sensitivities of over 100 recently published biosensors using various analytical techniques such as fluorescence, voltammetry, inductively coupled plasma techniques, spectrophotometry and visual colorimetric detection that display selectivity for copper, cadmium, lead, mercury and/or aluminium in aqueous solutions...
September 17, 2018: Biophysical Reviews
Evelyne Deplazes, David Poger, Bruce Cornell, Charles G Cranfield
At the 2017 meeting of the Australian Society for Biophysics, we presented the combined results from two recent studies showing how hydronium ions (H3 O+ ) modulate the structure and ion permeability of phospholipid bilayers. In the first study, the impact of H3 O+ on lipid packing had been identified using tethered bilayer lipid membranes in conjunction with electrical impedance spectroscopy and neutron reflectometry. The increased presence of H3 O+ (i.e. lower pH) led to a significant reduction in membrane conductivity and increased membrane thickness...
September 15, 2018: Biophysical Reviews
Harry W Rathbone, Jeffery A Davis, Katharine A Michie, Sophia C Goodchild, Neil O Robertson, Paul M G Curmi
The role of non-trivial quantum mechanical effects in biology has been the subject of intense scrutiny over the past decade. Much of the focus on potential "quantum biology" has been on energy transfer processes in photosynthetic light harvesting systems. Ultrafast laser spectroscopy of several light harvesting proteins has uncovered coherent oscillations dubbed "quantum beats" that persist for hundreds of femtoseconds and are putative signatures for quantum transport phenomena. This review describes the language and basic quantum mechanical phenomena that underpin quantum transport in open systems such as light harvesting and photosynthetic proteins, including the photosystem reaction centre...
September 13, 2018: Biophysical Reviews
Yoshitaka Nakayama, Ken-Ichi Hashimoto, Yasuyuki Sawada, Masahiro Sokabe, Hisashi Kawasaki, Boris Martinac
Corynebacterium glutamicum has been utilized for industrial amino acid production, especially for monosodium glutamate (MSG), the food-additive for the "UMAMI" category of taste sensation, which is one of the five human basic tastes. Glutamate export from these cells is facilitated by the opening of mechanosensitive channels in the cell membrane within the bacterial cell envelope following specific treatments, such as biotin limitation, addition of Tween 40 or penicillin. A long-unsolved puzzle still remains how and why C...
September 12, 2018: Biophysical Reviews
Boris Martinac, Navid Bavi, Pietro Ridone, Yury A Nikolaev, Adam D Martinac, Yoshitaka Nakayama, Paul R Rohde, Omid Bavi
Mechanical stimuli acting on the cellular membrane are linked to intracellular signaling events and downstream effectors via different mechanoreceptors. Mechanosensitive (MS) ion channels are the fastest known primary mechano-electrical transducers, which convert mechanical stimuli into meaningful intracellular signals on a submillisecond time scale. Much of our understanding of the biophysical principles that underlie and regulate conversion of mechanical force into conformational changes in MS channels comes from studies based on MS channel reconstitution into lipid bilayers...
September 4, 2018: Biophysical Reviews
James A Nichols, Hsien W Herbert Chan, Matthew A B Baker
Machine learning (ML) is a form of artificial intelligence which is placed to transform the twenty-first century. Rapid, recent progress in its underlying architecture and algorithms and growth in the size of datasets have led to increasing computer competence across a range of fields. These include driving a vehicle, language translation, chatbots and beyond human performance at complex board games such as Go. Here, we review the fundamentals and algorithms behind machine learning and highlight specific approaches to learning and optimisation...
September 4, 2018: Biophysical Reviews
Qian Peter Su, Lining Arnold Ju
The focus of the cell biology field is now shifting from characterizing cellular activities to organelle and molecular behaviors. This process accompanies the development of new biophysical visualization techniques that offer high spatial and temporal resolutions with ultra-sensitivity and low cell toxicity. They allow the biology research community to observe dynamic behaviors from scales of single molecules, organelles, cells to organoids, and even live animal tissues. In this review, we summarize these biophysical techniques into two major classes: the mechanical nanotools like dynamic force spectroscopy (DFS) and the optical nanotools like single-molecule and super-resolution microscopy...
August 18, 2018: Biophysical Reviews
Michelle P Christie, Bronte A Johnstone, Rodney K Tweten, Michael W Parker, Craig J Morton
The cholesterol-dependent cytolysins (CDCs) are a family of bacterial toxins that are important virulence factors for a number of pathogenic Gram-positive bacterial species. CDCs are secreted as soluble, stable monomeric proteins that bind specifically to cholesterol-rich cell membranes, where they assemble into well-defined ring-shaped complexes of around 40 monomers. The complex then undergoes a concerted structural change, driving a large pore through the membrane, potentially lysing the target cell. Understanding the details of this process as the protein transitions from a discrete monomer to a complex, membrane-spanning protein machine is an ongoing challenge...
August 16, 2018: Biophysical Reviews
Mehreen Ali, Tero Aittokallio
In-depth modeling of the complex interplay among multiple omics data measured from cancer cell lines or patient tumors is providing new opportunities toward identification of tailored therapies for individual cancer patients. Supervised machine learning algorithms are increasingly being applied to the omics profiles as they enable integrative analyses among the high-dimensional data sets, as well as personalized predictions of therapy responses using multi-omics panels of response-predictive biomarkers identified through feature selection and cross-validation...
August 10, 2018: Biophysical Reviews
A Beqqali
Alternative splicing is an important mechanism used by the cell to generate greater transcriptomic and proteomic diversity from the genome. In the heart, alternative splicing is increasingly being recognised as an important layer of post-transcriptional gene regulation. Driven by rapidly evolving technologies in next-generation sequencing, alternative splicing has emerged as a crucial process governing complex biological processes during cardiac development and disease. The recent identification of several cardiac splice factors, such as RNA-binding motif protein 20 and 24, not only provided important insight into the mechanisms underlying alternative splicing but also revealed how these splicing factors impact functional properties of the heart...
August 2018: Biophysical Reviews
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