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Trending Papers in biophysics

Light powered CO2 fixation in artificial chloroplasts
From Paper: Light-powered CO2 fixation in a chloroplast mimic with natural and synthetic parts
Tobias J. Erb
Hybrid approach catches lightPlant chloroplasts enclose two major photosynthetic processes: light reactions, which generate the energy carriers adenosine triphosphate and reduced nicotinamide dinucleotide phosphate (NADPH), and dark reactions, which use these molecules to fix carbon dioxide and build biomass. Miller et al. appropriated natural components, thylakoid membranes from spinach, for the light reactions and showed that these could be coupled to a synthetic enzymatic cycle that fixes carbon dioxide within water-in-oil droplets. The composition of the droplets could be tuned and optimized and the metabolic activity monitored in real time by NADPH fluorescence (see the Perspective by Gaut and Adamala). These chloroplast-mimicking droplets bring together natural and synthetic components in a small space and are amenable to further functionalization to perform complex biosynthetic tasks.Science, this issue p. 649; see also p. 587Nature integrates complex biosynthetic and energy-converting tasks within compartments such as chloroplasts and mitochondria. Chloroplasts convert light into chemical energy, driving carbon dioxide fixation. We used microfluidics to develop a chloroplast mimic by encapsulating and operating photosynthetic membranes in cell-sized droplets. These droplets can be energized by light to power enzymes or enzyme cascades and analyzed for their catalytic properties in multiplex and real time. We demonstrate how these microdroplets can be programmed and controlled by adjusting internal compositions and by using light as an external trigger. We showcase the capability of our platform by integrating the crotonyl–coenzyme A (CoA)/ethylmalonyl-CoA/hydroxybutyryl-CoA (CETCH) cycle, a synthetic network for carbon dioxide conversion, to create an artificial photosynthetic system that interfaces the natural and the synthetic biological worlds.Natural photosynthetic components power a synthetic CO2 fixation pathway in picoliter droplets.Natural photosynthetic components power a synthetic CO2 fixation pathway in picoliter droplets.
Submitted by plant biology
A novel protein-based clinical test for COVID-19 that can distinguish mild from severe infections
From Paper: Clinical classifiers of COVID-19 infection from novel ultra-high-throughput proteomics
  • This study highlights potential therapeutic targets that include complement factors, the coagulation system, inflammation modulators as well as pro-inflammatory signaling both upstream and downstream of interleukin 6
  • There are 27 proteinaceous biomarkers that are differentially expressed between WHO severity grades for COVID-19. This differential expression allows the protocol to distinguish between mild and severe cases of COVID-19
Submitted by Patrick Joyce
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Statistical Mechanics Characterization of Neuronal Mosaics
Luciano da Fontoura Costa, Fernando Rocha, Silene Maria Araujo de Lima
Published: Nov 2004
The spatial distribution of neuronal cells is an important requirement forachieving proper neuronal function in several parts of the nervous system ofmost animals. For instance, specific distribution of photoreceptors and relatedneuronal cells, particularly the ganglion cells, in mammal's retina is requiredin order to properly sample the projected scene. This work presents how twoconcepts from the areas of statistical mechanics and complex systems, namelythe \emph{lacunarity} and the \emph{multiscale entropy} (i.e. the entropycalculated over progressively diffused representations of the cell mosaic),have allowed effective characterization of the spatial distribution of retinalcells.
Retrieved from arxiv
Teardown of Tesla's Lithium-Ion Battery
From Paper: Aging of Tesla’s 18650 Lithium-Ion Cells: Correlating Solid-Electrolyte-Interphase Evolution with Fading in Capacity and Power
The long-term performance of commercial lithium-ion batteries used in today’s electric vehicles is of utmost importance forautomotive requirements. Here, we use Tesla’s 18650 cells manufactured by Panasonic to elucidate the origins of capacity fading andimpedance increase during both calendar and cycle aging. Full cell testing is systematically carried out at three different temperatures(25◦C, 40◦C, 60◦C). The cells are galvanostatically cycled at different C-rates (0.33 C – 1 C) and calendar aging is monitored at 4different state-of-charges (SOC). Operation at high temperatures turns out to have the largest effect on both the capacity and directcurrent (DC) impedance. As an example, after 500 cycles at 25◦C and 40◦C capacity fading is approximately 12%, while at 60◦C thefading reaches 22%. Our DC impedance measurements reveal the same trend. Post mortem analysis indicate that aging is stronglyrelated to changes of the solid electrolyte interphase (SEI). Hence, the changes in performance are correlated with the change incomposition (and thickness) of the SEI formed. In particular, we quantitatively measure the formation of electrically insulating LiFand find a correlation between overall DC impedance of the cells and lithium fluoride of the SEI.
Submitted by Tim Holme
Clearing-induced tissue shrinkage: Novel observation of a thickness size effect.
R.C.M. Vulders, R.C. Hoogenhuizen, E. Giessen, P.J. Zaag
Published: Apr 2020
The use of clearing agents has provided new insights in various fields of medical research (developmental biology, neurology) by enabling examination of tissue architecture in 3D. One of the challenges is that clearing agents induce tissue shrinkage and the shrinkage rates reported in the literature are incoherent. Here, we report that the shrinkage for a widely-used clearing agent decreases significantly with increasing sample size, and report an analytical description.### Competing Interest StatementRV and PJZ are employed by Royal Philips and may own company stock.
Retrieved from biorxiv
Disordered Proteins Enable Histone Chaperoning on the Nucleosome
Heidarsson, Pétur, et al
Published: Apr 2020
Proteins with highly charged disordered regions are abundant in the nucleus, where many of them interact with nucleic acids and control key processes such as transcription. The functional advantages conferred by protein disorder, however, have largely remained unclear. Here we show that disorder can facilitate a remarkable regulatory mechanism involving molecular competition. Single-molecule experiments demonstrate that the human linker histone H1 binds to the nucleosome with ultra-high affinity. However, the large-amplitude dynamics of the positively charged disordered regions of H1 persist on the nucleosome and facilitate the interaction with the highly negatively charged and disordered histone chaperone prothymosin α. Consequently, prothymosin α can efficiently invade the H1-nucleosome complex and displace H1 via competitive substitution. By integrating experiments and simulations, we establish a molecular model that rationalizes this process structurally and kinetically. Given the abundance of charged disordered regions in the nuclear proteome, this mechanism may be widespread in cellular regulation.### Competing Interest StatementThe authors have declared no competing interest.
Retrieved from biorxiv
Microbial-induced calcium carbonate precipitation: An experimental toolbox for in situ and real-time investigation of micro-scale pH evolution
Jennifer Zehner, Anja Røyne, Alexander Wentzel, Pawel Sikorski
Published: Apr 2020
Concrete is the second most consumed product by humans, after water. However, the production of cement, which is used as a binding material in concrete, causes more than 5% of anthropogenic CO2 emissions and has therefore a significant contribution to climate change and global warming. Due to increasing environmental awareness and international climate goals, there is a need for emission-reduced materials, that can replace conventional concrete in certain applications. One path to produce a solid, concrete-like construction material is microbial-induced calcium carbonate precipitation (MICP). As a calcium source in MICP, crushed limestone, which mainly consists out of CaCO3, can be dissolved with acids, for example lactic acid. The pH evolution during crystallization and dissolution processes provides important information about kinetics of the reactions. However, previous research on MICP has mainly been focused on macro-scale pH evolution and on characterization of the finished material. To get a better understanding of MICP it is important to be able to follow also local pH changes in a sample. In this work we present a new method to study processes of MICP at micro-scale in situ and in real time. We present two different methods to monitor the pH changes during the precipitation process of CaCO3. In the first method, the average pHs of small sample volumes are measured in real time, and pH changes are subsequently correlated with processes in the sample by comparing to optical microscope results. The second method is introduced to follow local pH changes at a grain scale in situ and in real time. Furthermore, local pH changes during the dissolution of CaCO3 crystals are monitored. We demonstrate that these two methods are powerful tools to investigate pH changes for both MICP precipitation and CaCO3 dissolution for knowledge-based improvement of MICP-based material properties.### Competing Interest StatementThe authors have declared no competing interest.
Retrieved from biorxiv
Employing NaChBac for cryo-EM analysis of toxin action on voltage-gated Na+ channels in nanodisc
Gao, Shuai, et al
Published: Apr 2020
NaChBac, the first bacterial voltage-gated Na+ (Nav) channel to be characterized, has been the prokaryotic prototype for studying the structure-function relationship of Nav channels. Discovered nearly two decades ago, the structure of NaChBac has not been determined. Here we present the cryo-EM analysis of NaChBac in both detergent micelles and nanodiscs. Under both conditions, the conformation of NaChBac is nearly identical to that of the potentially inactivated NavAb. Determining the structure of NaChBac in nanodiscs enabled us to examine gating modifier toxins (GMTs) of Nav channels in lipid bilayers. To study GMTs in mammalian Navs, we generated a chimera in which the extracellular fragment of the S3 and S4 segments in the second voltage-sensing domain from Nav1.7 replaces the corresponding sequence in NaChBac. Cryo-EM structures of the nanodisc-embedded chimera alone and in complex with HuwenToxin IV (HWTX-IV) were determined to 3.5 Å and 3.2 Å resolutions, respectively. Compared to the structure of HWTX-IV-bound human Nav1.7, which was obtained at an overall resolution of 3.2 Å, the local resolution of the toxin has been improved from ~ 6 Å to ~ 4 Å. This resolution enabled visualization of toxin docking. NaChBac can thus serve as a convenient surrogate for structural studies of the interactions between GMTs and Nav channels in a membrane environment.### Competing Interest StatementThe authors have declared no competing interest.
Retrieved from biorxiv
A nucleoid-associated protein bends and bridges DNA in a multiplicity of topological states with varying specificity
Yoshua, S., et al
Published: Apr 2020
Nucleoid-associated proteins perform crucial roles in compacting prokaryotic DNA, but how they generate higher-order nucleoprotein structures by perturbing DNA topology is unclear. Integration host factor, IHF, is a key nucleoid-associated protein in bacteria, creating sharp bends in DNA. We show that the IHF-DNA complex is more elaborate than a simple two-step model previously suggested and also provide structural insights about its multimodal nature. Using atomic force microscopy and molecular dynamics simulations we find three topological modes in roughly equal proportions: "associated" (73°), "half-wrapped" (107°) and "fully-wrapped" (147°), with only the latter occurring with sequence specificity. DNA bridging is seen not only with high IHF concentrations but also with densely packed binding sites, with simulations showing this occurs through another binding mode that does not depend on sequence. We present a model of these states and propose a crucial biological role for these observed behaviors.### Competing Interest StatementThe authors have declared no competing interest.
Retrieved from biorxiv
Distinct Structural Flexibility within SARS-CoV-2 Spike Protein Reveals Potential Therapeutic Targets
Serena Chen, M. Young, John Gounley, Christopher Stanley, Debsindhu Bhowmik
Published: Apr 2020
The emergence and rapid worldwide spread of the novel coronavirus disease, COVID-19, has prompted concerted efforts to find successful treatments. The causative virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), uses its spike (S) protein to gain entry into host cells. Therefore, the S protein presents a viable target to develop a directed therapy. Here, we deployed an integrated artificial intelligence with molecular dynamics simulation approach to provide new details of the S protein structure. Based on a comprehensive structural analysis of S proteins from SARS-CoV-2 and previous human coronaviruses, we found that the protomer state of S proteins is structurally flexible. Without the presence of a stabilizing beta sheet from another protomer chain, two regions in the S2 domain and the hinge connecting the S1 and S2 subunits lose their secondary structures. Interestingly, the region in the S2 domain was previously identified as an immunodominant site in the SARS-CoV-1 S protein. We anticipate that the molecular details elucidated here will assist in effective therapeutic development for COVID-19.### Competing Interest StatementThe authors have declared no competing interest.
Retrieved from biorxiv
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