JournalTOCs

Physical Biology
Journal Prestige (SJR): 0.756

Citation Impact (citeScore): 2
Number of Followers: 4

Hybrid journal (It can contain Open Access articles)
ISSN (Print) 1478-3975 - ISSN (Online) 1478-3975
Published by IOP

[45 journals]

Surviving early career research and beyond in biophysics/biological
physics: a concise user guide
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  Authors: Mark C Leake
  First page: 050201
  Abstract: Early career researcher (ECR) development is a dynamic challenge that tensions the urge to perform ground-breaking research against an ultimate practical aspiration of establishing an acceptable level of job security. There is no typical career path for an ECR, least of all in the area of biophysics/biological physics. Being explicitly interdisciplinary across the physical-life sciences interface presents more opportunities for a multiplicity of career trajectories through different home academic institutions and departments, as well as offering a broader range of alternative future career trajectories in non-academic sectors. That said, there are key common features, such as the transient nature of fixed-term postdoctoral contracts, the substantial research and domestic challenges that these present, and the often overwhelming pressures of the realities of competition in the job market. In this short article, I outline the key challenges to ECRs in this area and discuss simple strategies to manage and potentially overcome them. To highlight discussion, I draw from specific exemplars in the UK, however, the key guide applies globally to all ECRs in biophysics/biological physics.
  Citation: Physical Biology
  PubDate: 2022-07-10T23:00:00Z
  DOI: 10.1088/1478-3975/ac7373
  Issue No: Vol. 19, No. 5 (2022)
Instabilities of complex fluids with partially structured and partially
random interactions
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  Authors: Giorgio Carugno; Izaak Neri Pierpaolo Vivo
  First page: 056001
  Abstract: We develop a theory for thermodynamic instabilities of complex fluids composed of many interacting chemical species organised in families. This model includes partially structured and partially random interactions and can be solved exactly using tools from random matrix theory. The model exhibits three kinds of fluid instabilities: one in which the species form a condensate with a local density that depends on their family (family condensation); one in which species demix in two phases depending on their family (family demixing); and one in which species demix in a random manner irrespective of their family (random demixing). We determine the critical spinodal density of the three types of instabilities and find that the critical spinodal density is finite for both family condensation and family demixing, while for random demixing the critical spinodal density grows as the square root of the number of species. We use the developed framework to describe phase-separation instability of the cytoplasm induced by a change in pH.
  Citation: Physical Biology
  PubDate: 2022-07-12T23:00:00Z
  DOI: 10.1088/1478-3975/ac55f9
  Issue No: Vol. 19, No. 5 (2022)
Mechanical testing of particle streaming and intact extracellular mucilage
nanofibers reveal a role of elastic force in diatom motility
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  Authors: Braulio Gutiérrez-Medina; Ana Iris Peña Maldonado Jessica Viridiana García-Meza
  First page: 056002
  Abstract: Diatoms are unicellular microalgae with a rigid cell wall, able to glide on surfaces by releasing nanopolymeric fibers through central slits known as raphes. Here we consider the model Nitszchia communis to perform quantitative studies on two complementary aspects involved in diatom gliding. Using video microscopy and automated image analysis, we measure the motion of test beads as they are pulled by extracellular polymeric substances (EPS) fibers at the diatom raphe (particle streaming). A multimodal distribution of particle speed is found, evidencing the appearance of short-time events of high speed and acceleration (known as jerky motion) and suggesting that different mechanisms contribute to set diatom velocity during gliding. Furthermore, we use optical tweezers to obtain force-extension records for extracellular diatom nanofibers; records are well described by the worm-like chain model of polymer elasticity. In contrast to previous studies based on application of denaturing force (in the nN regime), application of low force (up to 6 pN) and using enable us to obtain the persistence length of intact fibers. From these measurements, mechanical parameters of EPS fibers such as radius and elastic constant are estimated. Furthermore, by modeling particle streaming as a spring in parallel with a dashpot, we show that the time involved in the release of mechanical energy after fiber detachment from beads (elastic snapping) agrees with our observations of jerky motion. We conclude that the smooth and jerky motions displayed by gliding diatoms correspond to molecular motors and elastic snapping, respectively, thus providing quantitative elements that incorporate to current models of the mechanics behind diatom locomotion.
  Citation: Physical Biology
  PubDate: 2022-07-13T23:00:00Z
  DOI: 10.1088/1478-3975/ac7d30
  Issue No: Vol. 19, No. 5 (2022)
Can biophysical models of dendritic spines be used to explore synaptic
changes associated with addiction'
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  Authors: Mayte Bonilla-Quintana; Padmini Rangamani
  First page: 041001
  Abstract: Effective treatments that prevent or reduce drug relapse vulnerability should be developed to relieve the high burden of drug addiction on society. This will only be possible by enhancing the understanding of the molecular mechanisms underlying the neurobiology of addiction. Recent experimental data have shown that dendritic spines, small protrusions from the dendrites that receive excitatory input, of spiny neurons in the nucleus accumbens exhibit morphological changes during drug exposure and withdrawal. Moreover, these changes relate to the characteristic drug-seeking behavior of addiction. However, due to the complexity of dendritic spines, we do not yet fully understand the processes underlying their structural changes in response to different inputs. We propose that biophysical models can enhance the current understanding of these processes by incorporating different, and sometimes, discrepant experimental data to identify the shared underlying mechanisms and generate experimentally testable hypotheses. This review aims to give an up-to-date report on biophysical models of dendritic spines, focusing on those models that describe their shape changes, which are well-known to relate to learning and memory. Moreover, it examines how these models can enhance our understanding of the effect of the drugs and the synaptic changes during withdrawal, as well as during neurodegenerative disease progression such as Alzheimer's disease.
  Citation: Physical Biology
  PubDate: 2022-06-13T23:00:00Z
  DOI: 10.1088/1478-3975/ac6cbe
  Issue No: Vol. 19, No. 4 (2022)
Extracellular matrix as a driver for intratumoral heterogeneity
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  Authors: Dharma Pally; Shyamili Goutham Ramray Bhat
  First page: 043001
  Abstract: The architecture of an organ is built through interactions between its native cells and its connective tissue consisting of stromal cells and the extracellular matrix (ECM). Upon transformation through tumorigenesis, such interactions are disrupted and replaced by a new set of intercommunications between malignantly transformed parenchyma, an altered stromal cell population, and a remodeled ECM. In this perspective, we propose that the intratumoral heterogeneity of cancer cell phenotypes is an emergent property of such reciprocal intercommunications, both biochemical and mechanical-physical, which engender and amplify the diversity of cell behavioral traits. An attempt to assimilate such findings within a framework of phenotypic plasticity furthers our understanding of cancer progression.
  Citation: Physical Biology
  PubDate: 2022-06-20T23:00:00Z
  DOI: 10.1088/1478-3975/ac6eb0
  Issue No: Vol. 19, No. 4 (2022)
Theoretical model of external spinal cord stimulation
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  Authors: Mikhail N Shneider; Mikhail Pekker
  First page: 044001
  Abstract: In this paper, a simple theoretical model of the excitation of action potentials of multiple motor pools by stimulating current pulses over the lumbosacral regions of the spinal cord is presented. The present model is consistent with known experimental data.
  Citation: Physical Biology
  PubDate: 2022-06-29T23:00:00Z
  DOI: 10.1088/1478-3975/ac768e
  Issue No: Vol. 19, No. 4 (2022)
One-dimensional acoustic potential landscapes guide the neurite outgrowth
and affect the viability of B35 neuroblastoma cells
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  Authors: Kathrin Baumgartner; Sophie C F Mauritz, Sebastian Angermann, Manuel S Brugger Christoph Westerhausen
  First page: 046005
  Abstract: On the way towards neuronal stimulation and signalling, standing surface acoustic waves (SSAWs) have become a widely used technique to create well-defined networks of living cells in vitro during the past years. An overall challenge in this research area is to maintain cell viability in long-term treatments long enough to observe changes in cellular functions. To close this gap, we here investigate SSAW-directed neurite outgrowth of B35 (neuroblastoma) cells in microchannels on LiNbO 3 chips, employing one-dimensional pulsed and continuous MHz-order SSAW signals at different intensities for up to 40 h. To increase the efficiency of future investigations, we explore the limits of applicable SSAW parameters by quantifying their viability and proliferation behaviour in this long-term setup. While cell viability is impaired for power levels above 15 dBm (32 mW), our investigations on SSAW-directed neurite outgrowth reveal a significant increase of neurites growing in preferential directions by up to 31.3% after 30 h of SSAW treatment.
  Citation: Physical Biology
  PubDate: 2022-06-12T23:00:00Z
  DOI: 10.1088/1478-3975/ac70a1
  Issue No: Vol. 19, No. 4 (2022)
Spatiotemporal feedforward between PKM2 tetramers and mTORC1 prompts
mTORC1 activation
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  Authors: Yu Xia; Shuming Wang, Chunbo Song Ruo-yu Luo
  First page: 046006
  Abstract: Most mammalian cells couple glucose availability to anabolic processes via the mTORC1 pathway. However, the mechanism by which fluctuations in glucose availability are rapidly translated into mTORC1 signals remains elusive. Here, we show that cells rapidly respond to changes in glucose availability through the spatial coupling of mTORC1 and tetramers of the key glycolytic enzyme pyruvate kinase M2 (PKM2) on lysosomal surfaces in the late G1/S phases. The lysosomal localization of PKM2 tetramers enables rapid increases in local ATP concentrations around lysosomes to activate mTORC1, while bypassing the need to elevate global ATP levels in the entire cell. In essence, this spatial coupling establishes a feedforward loop to enable mTORC1 to rapidly sense and respond to changes in glucose availability. We further demonstrate that this mechanism ensures robust cell proliferation upon fluctuating glucose availability. Thus, we present mechanistic insights into the rapid response of the mTORC1 pathway to changes in glucose availability. The underlying mechanism may be applicable to the control of other cellular processes.
  Citation: Physical Biology
  PubDate: 2022-06-12T23:00:00Z
  DOI: 10.1088/1478-3975/ac7372
  Issue No: Vol. 19, No. 4 (2022)
Minimal sensor arrays for localizing objects using an electric sense
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  Authors: Babak Pourziaei; Gregory M Lewis John E Lewis
  First page: 046007
  Abstract: Weakly electric fish encode perturbations in a self-generated electric field to sense their environment. Localizing objects using this electric sense requires that distance be decoded from a two-dimensional electric image of the field perturbations on their skin. Many studies of object localization by weakly electric fish, and by electric sensing in a generic context, have focused on extracting location information from different features of the electric image. Some of these studies have also considered the additional information gained from sampling the electric image at different times, and from different viewpoints. Here, we take a different perspective and instead consider the information available at a single point in space (i.e. a single sensor or receptor) at a single point in time (i.e. constant field). By combining the information from multiple receptors, we show that an object's distance can be unambiguously encoded by as few as four receptors at specific locations on a sensing surface in a manner that is relatively robust to environmental noise. This provides a lower bound on the information (i.e. receptor array size) required to decode the three-dimensional location of an object using an electric sense.
  Citation: Physical Biology
  PubDate: 2022-06-22T23:00:00Z
  DOI: 10.1088/1478-3975/ac75a5
  Issue No: Vol. 19, No. 4 (2022)
Peroxidation of tetronic 1107 reduces protein chaperone effect
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  Authors: Michelle X Ling; Michelle Nguyen, Colin A McFaul Raphael C Lee
  First page: 046008
  Abstract: To enhance the stability of protein therapeutics, pharmaceutical companies have long used various copolymer surfactants as excipients. They act to stabilize proteins by adhering to the hydrophobic surface of the protein preventing denaturation and aggregation. However, some commonly used excipients possess polyoxyalkylene chains that are susceptible to oxidative degradation while in aqueous solution. We postulate that oxidation reactions involving the hydrophobic domains reduce the surfactant's ability to stabilize the native protein structure. We investigated the effect of UV (λ = 254 nm) radiated poloxamine T1107 (T1107) on its ability to disaggregate DTT denatured hen egg-white lysozyme (HEWL). Peroxidation of UV irradiated T1107 was analyzed using FTIR spectroscopy, the Fe +2 to Fe +3 ion reduction assay method, and 1 H NMR. Our results indicate that increased UV irradiation led to structural changes in T1107, specifically the addition of a carbonyl on the formate group. The structural change decreased T1107's ability to disaggregate HEWL thus supporting our hypothesis. These results indicate that peroxide content is an important parameter to control in polyoxyalkylene-based excipients.
  Citation: Physical Biology
  PubDate: 2022-06-27T23:00:00Z
  DOI: 10.1088/1478-3975/ac6eaf
  Issue No: Vol. 19, No. 4 (2022)