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Paper materials with good biocompatibility, porous structures, hydrophilic property, capillary effect, low non-specific binding, and multi-modification have been widely applied in diagnostic devices for environmental monitoring, food safety, and healthcare. However, utilizing these properties on one paper chip for quantitative measurement of nucleic acid amplification from blood is a big challenge for point-of-care (POC) device. Here we report an integrative paper-based molecular diagnostic device (IPMD) with the capability of fast plasma separation and sensitive nucleic acid (NA) detection of HIV from blood. The IPMD is composed of a highly efficient plasma generation membrane over a rapid flow nitrocellulose layer for plasma separation, HIV NA collection, amplification, and fluorescence read-out. 100 μL of whole blood sample is separated on-chip within 5 min. The hydrophilic, porous, capillary properties of nitrocellulose are beneficial to pre-store all the chemical components of nucleic acid amplification by a lyophilization process. HIV NA with a limit-of-detection of 10 copies is achieved by analyzing the fluorescence intensity of the nitrocellulose layer after NA amplification for 20 min. These results suggest that our IMPD platform can promote the development of POC devices for global healthcare and personalized medicine.

Motivation Global protein surface comparison (GPSC) studies have been limited compared to other research works on protein structure alignment/comparison due to lack of real applications associated with GPSC. However, the technology advances in cryo-electron tomography (CET) have made methods to identify proteins from their surface shapes extremely useful. Results In this study, we developed a new method called Farthest point sampling (FPS)-enhanced Triangulation-based Iterative-closest-Point (ICP) (FTIP) for GPSC. We applied it to protein classification using only surface shape information. Our method first extracts a set of feature points from protein surfaces using FPS and then uses a triangulation-based efficient ICP algorithm to align the feature points of the two proteins to be compared. Tested on a benchmark dataset with 2329 proteins using nearest-neighbor classification, FTIP outperformed the state-of-the-art method for GPSC based on 3D Zernike descriptors. Using real and simulated cryo-EM data, we show that FTIP could be applied in the future to address problems in protein identification in CET experiments. Availability and implementation Programs/scripts we developed/used in the study are available at http://ani.stat.fsu.edu/∼yuan/index.fld/FTIP.tar.bz2. Supplementary information Supplementary data are available at Bioinformatics online.

A short segment of the disordered p53 transactivation domain (p53TAD) forms an amphipathic helix when bound to the E3 ubiquitin ligase, MDM2. In the unbound p53TAD, this short segment has transient helical secondary structure. Using a method that combines broad sampling of conformational space with re-weighting, it is shown that it is possible to generate multiple, independent structural ensembles that have highly similar secondary structure distributions for both p53TAD and a P27A mutant. Fractional amounts of transient helical secondary structure were found at the MDM2 binding site that are very similar to estimates based directly on experimental observations. Structures were identified in these ensembles containing segments that are highly similar to short p53 peptides bound to MDM2, even though the ensembles were re-weighted using unbound experimental data. Ensembles were generated using chemical shift data (alpha carbon only, or in combination with other chemical shifts) and cross-validated by predicting residual dipolar couplings. We think this ensemble generator could be used to predict the bound state structure of protein interaction sites in IDPs if there are detectable amounts of matching transient secondary structure in the unbound state.

Motivation: Outer membrane beta-barrels (OMBBs) are the proteins found in the outer membrane of bacteria, mitochondria and chloroplasts. There are thousands of beta-barrels reported in genomic databases with ∼2–3% of the genes in gram-negative bacteria encoding these proteins. These proteins have a wide variety of biological functions including active and passive transport, cell adhesion, catalysis and structural anchoring. Of the non-redundant OMBB structures in the Protein Data Bank, half have been solved during the past 5 years. This influx of information provides new opportunities for understanding the chemistry of these proteins. The distribution of charges in proteins in the outer membrane has implications for how the mechanism of outer membrane protein insertion is understood. Understanding the distribution of charges might also assist in organism selection for the heterologous expression of mitochondrial OMBBs. Results: We find a strong asymmetry in the charge distribution of these proteins. For the outward-facing residues of the beta-barrel within regions of similar amino acid density for both membrane leaflets, the external side of the outer membrane contains almost three times the number of charged residues as the internal side of the outer membrane. Moreover, the lipid bilayer of the outer membrane is asymmetric, and the overall preference for amino acid types to be in the external leaflet of the membrane correlates roughly with the hydrophobicity of the membrane lipids. This preference is demonstrably related to the difference in lipid composition of the external and internal leaflets of the membrane. Contact: joanna.slusky@fccc.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Microtubule associated protein 1 light chain 3B (LC3/ATG8) functions in autophagosome formation and autophagy substrate recruitment. LC3 exists in both a soluble (autophagosome-independent) form as well as a lipid modified form that becomes tightly incorporated into autophagosomal membranes. Although LC3 is known to associate with tens of proteins, relatively little is known about soluble LC3 aside from its interactions with the LC3 lipid conjugation machinery. In previous studies we found autophagosome-independent GFP-LC3 diffuses unusually slowly for a protein of its size, suggesting it may be constitutively associated with a high molecular weight complex, form homo-oligomers or aggregates, or reversibly bind microtubules or membranes. To distinguish between these possibilities, we characterized the size, stoichiometry, and organization of autophagosome-independent LC3 in living cells and in cytoplasmic extracts using Fluorescence Recovery After Photobleaching (FRAP) and Fluorescence Polarization Fluctuation Analysis (FPFA). We found that the diffusion of autophagosome-independent LC3 was unaffected by either mutational disruption of its lipid modification or microtubule depolymerization, suggesting this form of LC3 does not reversibly bind to microtubules or membranes. Brightness and homoFRET analysis indicate LC3 does not homo-oligomerize, ruling out this as a possibility for its slow diffusion. In contrast, mutation of specific residues on LC3 required for binding other proteins and mRNA led to changes in the effective hydrodynamic radius of the protein as well as its stoichiometry. This suggests that LC3 associates with a multi-component complex consisting of either proteins or RNA. We conclude that autophagosome-independent LC3 associates with a complex with an effective size of ∼500 kDa in the cytoplasm. These findings provide new insights into the nature of autophagosome-independent LC3 and illustrate the power of FRAP and FPFA to provide novel insights into the emergent properties of protein complexes in the autophagy pathway.

Aim: This study was performed to determine the effect of Hydroxychloroquine on visual system in patients with systemic lupus erythematosus.Materials and methods: In a cross -sectional study, 50 subjects (without visual problem and seizure) including 25 with and 25 without systemic lupus erythematosus under treatment with chloroquine were selected. Visual evoked potential test was performed in two groups.Results: The mean amplitude was 6.04 in case and 5.84 μ∉- ι∈1/2 χo∈1/2∉"ρoΔ γρo∉..π ωηιχη σηoωσ ∈1/2o σ∉"α∉"ισ∉"ιχαΔΔψ σιγ∈1/2ιϕιχα∈1/2∉" διϕϕeρe∈1/2χe.The mean latency was 100.50 in case and 95.35 msec in control group which is not statistically significant.Conclusion: Based on the result of present work one can conclude that hydroxychloroquine has no adverse effect on visual pathway which will be discussed in detail in full paper.

Herein, we propose a modified version of the Wako-Saitô-Muñoz-Eaton (WSME) model. The proposed model introduces an empirical temperature parameter for the hypothetical structural units (i.e., foldons) in proteins to include site-dependent thermodynamic behavior. The thermodynamics for both our proposed model and the original WSME model were investigated. For a system with beta-hairpin topology, a mathematical treatment (contact-pair treatment) to facilitate the calculation of its partition function was developed. The results show that the proposed model provides better insight into the site-dependent thermodynamic behavior of the system, compared with the original WSME model. From this site-dependent point of view, the relationship between probe-dependent experimental results and model's thermodynamic predictions can be explained. The model allows for suggesting a general principle to identify foldon behavior. We also find that the backbone hydrogen bonds may play a role of structural constraints in modulating the cooperative system. Thus, our study may contribute to the understanding of the fundamental principles for the thermodynamics of protein folding.

In the past decade a significant amount of research and development has been geared towards water treatment and distribution, especially in low income areas. Large fractions of this research have focused on waterborne contaminant removal, such as filters and flocculation agents, and biosensors designed to detect waterborne threats. In low income areas many of the currently used treatment methods are not suitable as they commonly are more expensive and difficult to maintain. Problems have also been observed with biosensors including a very low sensitivity, making it difficult to get accurate readings when low bacteria concentrations are present. In an attempt to address both of these problems in conjunction with one another, we have been studying the effects of a natural compound extracted from the Opuntia ficus-indica cactus as a flocculation and concentration agent for bacteria suspended in water. This material, known as mucilage, has proven to be an effective tool for aggregating and removing the sediment kaolin, and has also demonstrated flocculation of E. coli, B. cereus and B. subtilis. In bacteria treated columns thus far, the response in mucilage treated columns was almost immediate and large flocs were observed to form both with the naked eye and using a light microscope. Removal rates of up to 97% were also observed. Current tests with B. anthracis (fully attenuated) also demonstrate a great potential for mucilage in the fields of water treatment and biosensors. The aggregated bacteria that are formed within the column settle to the bottom forming a compact pellet that can then be removed for testing with biosensors. This type of flocculating agent has the potential to be very valuable in both of these fields because it is inexpensive, sustainable and easy to process and use.

Transmembrane β-barrels (TMBB) belong to a special structural class of proteins predominately found in the outer membranes of Gram-negative bacteria, mitochondria, and chloroplasts. TMBBs are surface-exposed proteins that perform a variety of functions ranging from iron acquisition to osmotic regulation. These properties suggest that TMBBs have great potential for use in vaccine or drug therapy development. Membrane proteins, such as TMBBs, are notoriously difficult to identify and characterize using traditional experimental approaches due to a variety of technical limitations. However, in silico prediction methods have been considered for handling the task of identifying the enigmatic sequences which fold into TMBBs. A prediction method based on the physicochemical properties of experimentally characterized TMBB structures was developed to predict TMBB-encoding genes from genomic databases. The algorithm's prediction efficiency was tested using a non-redundant set of sequences from proteins of known structure. The algorithm was based on the work of Wimley (2002), but was greatly improved because of its disappointingly high false-positive prediction rate and thusly renamed the Freeman-Wimley algorithm. The improved prediction algorithm developed in this study was shown to be more accurate than previously published prediction methods. Its accuracy is 99% when using the most efficient prediction criteria, i.e. the threshold where the most known TMBBs are correctly predicted and the most non-TMBBs are correctly excluded. The Freeman-Wimley algorithm was used to make predictions in 611 bacterial chromosomes, where an average of 3% of the genes in a given genome encoded TMBBs.

A hydrophobic filter paper of a given pore size containing a synthetic lipid, i.e. dioleyl phosphate, was interposed between aqueous electrolyte solutions having the same chemical composition and temperature. The electric capacitance and conductance of the membrane immersed in various concentrations of KCl were measured in the frequency range from 20 to 3 x 10(6) cycle/sec. The observed capacitance and conductance were found to be strongly dependent on the applied frequency. A theory is proposed to account for this dispersion of impedance observed in the present membrane-electrolyte system. The dispersion is attributed to the formation of bilayer membranes of the lipid inside the filter paper. The effects of the salt concentration, the adsorbed quantity of the lipid, and the pore size of the filter paper on the capacitance and conductance of the membrane are discussed in terms of the distribution function of bilayers formed within the filter paper.

Absolute thermodynamic efficiencies of conversion of light energy into chemical-free energy of molecular hydrogen by intact microalgae have been measured with an original physical measuring technique using a tin-oxide semiconducting gas sensor. Thin films of microalgae comprising of 5 to 20 cellular monolayers have been entrapped on filter paper, thereby constraining them in a well-defined circular geometry. Based on absolute light absorption of visible polychromatic illumination in the low-intensity region of the light saturation curve, conversion efficiencies of 6 to 24% have been obtained. These values are the highest ever measured for hydrogen evolution by green algae.

Solutions of Haemophilus influenzae transforming DNA were irradiated at temperatures ranging from 25 degrees C to - 196 degrees C. Temperature dependence of the formation of thymine-containing dimers was closely correlated with inactivation of transforming activity; in general, both dimerization and inactivation decreased with decreasing temperature. The fraction of nonphotoreactivable damage increased with increasing dose at low temperatures. The nonphotoreactivable spore-type photoproduct was formed at low temperatures with a maximum at - 100 degrees C, a temperature at which the nonphotoreactivable biological inactivation was also a maximum. Intrastrand cross-linking, like dimer formation, decreased with decreasing irradiation temperature.

Radioautography and extractive techniques were used to analyze the transport of cysteamine phosphate and its derivatives in salamander oocytes. The quantitative relations among the processes involved — membrane permeation, enzymatic dephosphorylation, binding through mixed disulfide formation, and cytoplasmic diffusion — were elucidated. Within the detection limits, all of the intracellular material is present as dephosphorylated derivatives. Cytoplasmic diffusion is effectively slowed by binding (the “chromatographic” effect) and makes an appreciable contribution to cellular flux rates. As a consequence, one can observe by radioautography a cortical diffusion ring which spreads inward as a function of influx time, while also increasing in peak density because of the finite membrane permeability. Good agreement was found between the transport parameters determined by radioautography and those from influx data for the whole oocyte. The ratio of nuclear to cytoplasmic concentrations of the cysteamine phosphate derivatives at equilibrium is about 0.4. The nuclear membrane is, however, a negligible barrier to transport, and the asymmetry appears to arise primarily from the quantity and sulfhydryl content of the binding proteins in the two compartments.

The technique of alkaline sucrose gradient centrifugation was used to study newly synthesized DNA in control and ultraviolet light-irradiated mouse L, human HeLa, and Chinese hamster ovary cells. Nascent DNA molecular weight distributions did not appear to differ among the three cell lines for unirradiated cells. However, at short times after ultraviolet light irradiation, human HeLa cells appeared to synthesize more low molecular weight DNA than either mouse L or Chinese hamster ovary cells. Since this difference was not related to differences in either the rate of DNA synthesis or amount of ultraviolet damage in the irradiated cells it appeared to be a phenotypic characteristic of the cell lines tested. A parallel was noted for these three cell lines between an increase in the synthesis of low molecular weight DNA, detected on alkaline sucrose gradients, and cell killing as measured by the ability of irradiated cells to form colonies.

The value of the products and chemicals made from the 10% of fossil oil that is used as feed stock in the chemical industry is the same as the value of all fuel made from the remaining 90%. Using plant oil instead of fossil oil as feed stock for the materials and chemicals could capture much of this added value, if the plant molecules are optimized in-planta for the end use and thereby minimizing the downstream processing costs. I have a vision that within 20 years time replace 40% of the fossil oil used in the chemical industry with renewable plant oils, whilst ensuring that growing demand for food oils is also met. This will require a trebling of global plant oil production from current levels of 135 MT to about 400 MT annually. Realisation of this potential will rely on application of plant biotechnology to (a) tailor plant oils to have high purity (preferably > 90%) of single desirable fatty acids, (b) introduce unusual fatty acids that have speciality end-use functionalities, (c) increase plant oil production capacity by increased oil content in current oil crops, and conversion of other high biomass crops into oil accumulating crops. Using plant oils in the chemical industry will not only enable replacement of fossil oil but will, at least equally importantly, enable substantial overall energy savings and generate added-value for agricultural products that cannot be captured by using them for energy production. I will in this presentation outline research strategies for the replacement of a significant portion of the fossil oil used in the chemical industry with plant oils by extrapolating on the present state of the art of science in the area.

We report on DNA translocations through nanopores created in graphene membranes. Devices consist of 1-5 nm thick graphene membranes with electron-beam sculpted nanopores from 5 to 10 nm in diameter. Due to the thin nature of the graphene membranes, we observe larger blocked currents than for traditional solid-state nanopores. However, ionic current noise levels are several orders of magnitude larger than those for silicon nitride nanopores. These fluctuations are reduced with the atomic-layer deposition of 5 nm of titanium dioxide over the device. Unlike traditional solid-state nanopore materials that are insulating, graphene is an excellent electrical conductor. Use of graphene as a membrane material opens the door to a new class of nanopore devices in which electronic sensing and control are performed directly at the pore.

In the last decade an extraordinary amount of research and development has focused on alleviating problems associated with contaminated water. With the majority of the World's population living on the brink of illness due to bacterial contamination in town water supplies, much of this attention has been focused on bacteria removal and sensors. Many current decontamination techniques are too technologically advanced for less developed countries, often resulting in their rejection by the societies they serve. Sensor work has also come across problems including poor sensitivity making it difficult to detect microorganisms at low concentrations. We have been testing a material extracted from the Opuntia ficus-indica cactus which could possibly address both of these problems in conjunction with one another. This material, referred to as cactus mucilage, has proven itself in the past as a viable flocculating agent for use in water contaminated with sediments and heavy metals. Flocculation tests, now focused on Bacillus cereus and Escherichia coli, have also given insight on the mucilage's ability to gather and concentrate bacterial contaminants from ion-rich water supplies. In columns with bacteria suspended in hard and soft water, flocculation begins immediately and is complete in approximately five to ten minutes with concentration rates of up to 99%. In addition to cleaning the water, the flocs formed with the mucilage could be removed from the water for sensor use. Cactus mucilage is an ideal material for water treatment and assessment because it is a naturally occurring, low cost material that is easy to obtain, process and use. Using this type of green chemistry, not only are bacteria concentrations significantly lowered in contaminated water, but also a highly concentrated volume of bacteria is produced that could potentially aid in biosensors.

On February 20, 1996, a workshop titled "Advances in Sedimentation Velocity Analysis" was held at the Biophysical Society meeting in Baltimore, Maryland, in honor of Professor David Yphantis's 65th birthday. Although he is known more for his work with sedimentation equilibrium, David's work on instrumentation and data analysis is the foundation for many of the recent advances in both equilibrium and velocity sedimentation. Over the years he has trained numerous graduate students, most of whom have gone on to emphasize the use of analytical ultracentrifugation to answer biochemical questions involving macromolecular assembly. His laboratory was one of very few that continued to use and develop analytical ultracentrifugation during its nadir in the 1970s and early 1980s. The rebirth and resurgence of analytical ultracentrifugation owe a great deal to his persistence and enthusiasm. These efforts have borne fruit. In the last five years, through his work at the National Analytical Ultracentrifugation Facility, he has helped train nearly 100 individuals in the delicate art of nonlinear least-squares analysis of equilibrium sedimentation data. Furthermore, the number of researchers using the ultracentrifuge and the number of papers published has skyrocketed in the last few years. This workshop, then, was a way to thank David for his years of devotion to analytical ultracentrifugation.

The effectiveness of outer hair cells (OHCs) in amplifying the motion of the organ of Corti, and thereby contributing to the sensitivity of mammalian hearing, depends on the mechanical power output of these cells. Electromechanical coupling in OHCs, which enables these cells to convert electrical energy into mechanical energy, has been analyzed in detail using isolated cells using primarily static membrane models. In the preceding reports, mechanical output of OHC was evaluated by developing a kinetic theory based on a simplified onedimensional (1D) model for OHCs. Here such a kinetic description of OHCs is extended by using the membrane model, which has been used for analyzing in vitro experiments. The present theory predicts, for systems without inertial load, that elastic load enhances positive shift of voltage dependence of the membrane capacitance due to turgor pressure. For systems with inertia, mechanical power output also depends on turgor pressure. The maximal power output is, however, similar to the previous prediction of up to ∼10 fW based on the 1D model.Statement of SignificanceThis paper is an attempt for developing a physical model to clarify the mechanism of outer hair cells in performing their role as an amplifier in mammalian hearing. Specifically, this paper extends a static model of these cells into a dynamic one to evaluate mechanical power production, which is essential for the function of these cells. It clarifies the assumptions essential for a previous phenomenological theory, a 1-D model. In addition, it describes the effect of turgor pressure on mechanical power generation.

Blotting has been the standard technique for preparing aqueous samples for single-particle electron cryo-microscopy for over three decades. This technique removes the excess solution from a transmission electron microscope grid by pressing absorbent filter paper against the specimen before vitrification. However, this standard technique produces vitreous ice with inconsistent thickness from specimen to specimen and from region to region within the same specimen, the reasons for which are not understood. Here, high-speed interference contrast microscopy is used to demonstrate that the irregular pattern of fibers in the filter paper imposes tortuous, highly variable boundaries during the removal of excess liquid from a flat, hydrophilic surface. As a result, aqueous films of nonuniform thickness are formed while the filter paper is pressed against the substrate. This pattern of nonuniform liquid thickness changes again after the filter paper is pulled away, but the thickness still does not become completely uniform. We suggest that similar topographical features of the liquid film are produced during the standard technique used to blot EM grids and that these manifest in nonuniform ice after vitrification. These observations suggest that alternative thinning techniques, which do not rely on direct contact between the filter paper and the grid, may result in more repeatable and uniform sample thicknesses.

During clathrin-mediated endocytosis, a patch of flat plasma membrane is deformed into a vesicle. In walled cells, such as plants and fungi, the turgor pressure is high and pushes the membrane against the cell wall, thus hindering membrane internalization. In this paper, we study how a patch of membrane is deformed against turgor pressure by force and by curvature-generating proteins. We show that a large amount of force is needed to merely start deforming the membrane and an even larger force is needed to pull a membrane tube. The magnitude of these forces strongly depends on how the base of the membrane is constrained and how the membrane is coated with curvature-generating proteins. In particular, these forces can be reduced by partially but not fully coating the membrane patch with curvature-generating proteins. Our theoretical results show excellent agreement with experimental data.SIGNIFICANCEYeast cells have been widely used as a model system to study clathrin-mediated endocytosis. The mechanics of membrane during endocytosis has been extensively studied mostly in low turgor pressure condition, which is relevant for mammalian cells but not for yeast cells. It has been suggested that as a result of high turgor pressure in yeast cells, a large amount of force is needed to drive the progress of the membrane invagination. In this paper, we investigated biologically relevant mechanisms to reduce the force requirement. We highlight the role of boundary conditions at the membrane base, which is a factor that has been largely ignored in previous studies. We also investigate the role of curvature-generating proteins and show that a large protein coat does not necessarily reduce the force barrier for endocytosis.

For established journals, especially nonprofit journals sponsored by scientific societies, the greatest challenge in scientific publishing has been the explosive proliferation of new journals and, relatedly, the rise of the megajournals. These journals rely on Author Processing Charges (APCs) for revenue and are, therefore, financially incentivized to publish as many articles as possible. The two major megajournals published almost 45,000 papers in 2016. Why do authors flock to submit their papers to these mass-produced publications? I find this especially perplexing, given the stated policy of these journals to ignore significance or importance in deciding what to publish. Part of the allure may be that these journals do make it easy for authors to get their papers published and offer a direct pipeline after a paper may have been declined by a more prestigious journal within their corporate stables. As an independent journal, owned by a relatively small society, Biophysical Journal is unable to offer some of these conveniences. However, I’m already detecting that the novelty is wearing off of these scientific publishing factories.Going forward, in the face of the aforementioned disruptive trends in scientific publishing, we need to continue to assure the highest quality and find innovative ways to enhance the journal’s vitality. This means continuing to emphasize that only the best science will be accepted for publication in our journal. It means promoting the outstanding peer review process, led by empathetic volunteer editors who are leaders in their fields. It means finding new ways to enhance the journal content to engage our readers and target a wider readership. And it means continuing to strengthen the connection between Biophysical Journal and the membership of the Biophysical Society.I’m confident that all of these goals will be fully embraced under the able leadership of our incoming Editor-in-Chief, Jane Dyson. I’ve had the pleasure of working closely and collaboratively with her over the last few months as we transition. I am convinced she has the wisdom, commitment, and creativity to take BJ to new heights.Throughout this editorial, I very deliberately used the word “we” to describe the accomplishments of the last five years. For each accomplishment, it was very definitely a collaborative effort both in conceptualization and implementation, and it is a pleasure to close by acknowledging the individuals who comprise Team BJ. Beth Staehle has now been with BJ as Publications Manager for four years. She is a consummate professional who has been an extraordinarily wise, sensitive, and steady hand at managing any issue that comes along. Her dedication is regularly demonstrated by emails appearing in my inbox on weekends or late into the evening. She is willing to respond to any request, no matter how simple or complex, whether from author, editor, reviewer, or reader. Importantly, she is also a crucial resource to both generate and critique new ideas. Our journal is truly fortunate to have Beth in the driver’s seat. The daily operations of the journal are in the able hands of Catie Curry and Tara Singh; they are proactive and conscientious in overseeing interactions with authors, reviewers, and editors. The BPS Executive Officer, Ro Kampman, is always available to give her sage advice; her tireless work for the society is truly remarkable. The quality and integrity of the journal is assured by our outstanding editorial board of 130 volunteer scientists; they have been led by Associate Editors Tamar Schlick, Liz Rhoades, Michael Pusch, Dave Piston, Claudia Steinem, Stas Shvartsman, Mike Ostap, Brian Salzberg, and, until this year, Nathan Baker. It is because of our dedicated editorial board that only the highest quality biophysics gets published in our journal and that authors so often express their appreciation for the constructive review process. The behind the scenes work of the Cell Press team, led by Keith Wollman, generously provides a wealth of resources, expertise, and guidance in marketing, press releases, web technology, webinars, collections, and interactive content. I have had a most productive relationship with the BPS Publications Committee, especially through its leaders Olaf Andersen and Da-Neng Wang. Many of the initiatives undertaken over the last five years were developed through the advice and consent of the Publications Committee and Olaf and Da-Neng were real partners in the leadership of our journal.In these difficult times for science, where not only stable funding support but the very value of the scientific enterprise is being challenged, it has never been more important to assure that scientific findings are published with transparency, accuracy, and after rigorous peer review. Thankfully, the biophysics community can fully rely on its society journal with its volunteer scientist editors to shoulder this important responsibility. My gratitude goes to the Biophysical Society for giving me the privilege of leading our journal for the past five years. Working with the journal staff, editorial board, and the BPS has made this a truly rewarding job.

RNA's rising stardom is well-justified by its structural variability and functional versatility. Indeed, besides RNA's key role in the translational machinery, RNA is instrumental for the manipulation and regulation of genetic information. Because regulatory errors and altered RNA functions can trigger abnormal cellular events, RNA has also emerged as a strong drug target for treating a variety of human diseases. Of course, fundamental mechanistic knowledge of RNA folding, energetics, and kinetics is essential for understanding RNA's pathways into its many functional states and how these states are affected by ions, proteins, and other nucleic acid entities in the cellular milieu. Such information is important for deploying RNA features into targeted therapy using nucleic acid targets rather than proteins and other compounds.Our understanding of these fundamental aspects of RNA activity has advanced in recent years due to significant improvements in experimental structural determination of RNAs as well as focused computational efforts that explore RNA structure and motion. The combined knowledge has led to many efforts in RNA design, with applications in medicine and technology.This special volume in Biophysical Journal celebrates the many innovative approaches in RNA science, while also presenting the challenges in RNA structural modeling and design. Papers were invited by scientists who are advancing the field on both genomic and molecular levels of RNA using novel experimental, mathematical, statistical, and computational approaches.In our perspective article (Schlick and Pyle), we provide an overview of current RNA topics and point to open questions, including RNA structural assemblies (hierarchical folding, multiple conformational states and their clustering), RNA motifs, and chemical reactivity of RNA, as used for structural prediction and functional inference.We also discuss the software and database issues associated with RNA structures: motif annotation, database updating, and quality control of RNA structures. We mention various modeling approaches for structure prediction, mechanistic analysis of RNA reactions, and RNA design. In particular, we highlight the complementary roles that both atomistic and coarse-grained approaches play in such simulations.Among the research articles in this collection, many deal with the complex landscapes and structural assemblies of RNA, and RNA's conformational variability.Four papers, in particular, focus on the effect divalent ions and/or other molecular components for the assembly of RNA complexes. Falkenberg and colleagues (Carson et al.) develop an innovative deterministic-stochastic-statistical modeling approach to study RNA granules, ensembles of specific RNA, and proteins; their work offers mechanistic insight into the function of RNA granules in eukaryotic transcription.Mitra and co-workers (Halder et al.) use density functional quantum-mechanical computations to study the modes of magnesium ion binding in RNAs containing reverse Watson-Crick base pairs. They find that the ions can modulate the base pair geometries in a variety of sequence contexts.Bergonzo and Cheatham show by classical molecular dynamics simulations how divalent ions can stabilize geometries within the Varkud Satellite ribozyme so that the RNA junction in the structure acts a scaffold.With Roy and Onuchic, Sanbonmatsu similarly uses large-scale atomic molecular dynamics simulations of the SAM riboswitch RNA to reveal the importance of divalent ions in coordinating a pseudoknot motif motion that is significant to transcription regulation.The separate groups of Mathews (Tan et al.), Heitsch (Rogers et al.), and Laederach (Woods et al.) present new approaches to predict or assess the conformational landscape of RNA secondary structural elements. Although secondary-structure (2D) prediction algorithms have improved in recent years through the incorporation of experimental data from chemical probing and cross-linking methods like SHAPE (Selective 2′-OH acylation by primer extension), for example, challenges arise in evaluating the complex landscape of 2D structures, since many local minima may be biologically relevant.Tan et al. present an algorithm for 2D structure prediction that uses comparative sequence analysis and chemical mapping data called TurboFold II.Rogers et al. present a numerical analysis model that helps measure the conditioning and robustness of the Boltzmann ensemble of minimum-free-energy states in the 2D landscape of RNAs. Woods et al. describe a robust approach for visualizing the conformational ensemble of RNAs based on clustering and evaluating ensembles for a family of mutant sequences; their application to an RNA riboswitch generates profiles that correlate with structural rearrangements consistent with the RNA's function.The theme of structural variability is also exemplified in the cluster analysis work of Lindorff-Larsen and Botaro, who reveal the versatility of sequence and tertiary interactions involved defining RNA tetraloops.A different theme of RNA structural assemblies is the focus of two experimental works from the groups of Lanier (Roy et al.) and Knobler (Beren et al.).Roy et al. explore ribosomal RNA (rRNA) interactions with protein factors to determine the extent by which rRNA folds independently of the proteins with which it binds in the complex. Their results highlight the folding autonomy of rRNA, whereby the protein cofactors act as co-chaperones, providing evidence for the RNA-world hypothesis.Beren et al. use various experimental techniques to analyze the assembly of the cowpea chlorotic mottle virus (CCMV). They show that the structure of the capsid protein of CCMV formed during the self-assembly of the CCMV virus-like particles depends critically on the 2D structure of the RNA molecule and its absence, highlighting the importance of RNA's 2D structures in biological structure and activity.Besides atomic models, lower-resolution (or coarse-grained) models have been successful at modeling RNA, specifically for predicting tertiary structures and for pursuing design applications.Pasquali and co-workers explore how human intuition might play a role in problem solving by employing their group's coarse-grained model for RNA combined with experience in open software they developed for students. Their study suggests that human instinct could be deployed to fold simple but non-trivial tertiary RNA topologies. Such studies open the way for further scientific discovery by open source scientific games that started for proteins (like “folding at home'').A new coarse-grained model for RNA, focused on studying RNA interactions, is presented by Marrink and colleagues.As this collection shows, scientists from varied disciplines are increasingly drawn into RNA's unique challenges, which are benefitting from the growing experimental information on RNA structural variability and function, along with the various mathematical, statistical, and kinetic approaches for RNA investigations. We can only anticipate more exciting research and discoveries on RNA, as well as applications to human disease treatment in the coming years. We hope you will enjoy these papers.

The Biophysical Journal welcomes 24 new members to the Editorial Board, beginning January 1, 2017. Editorial Board members are all working scientists who volunteer their time to maintain the quality of the journal by assuring fair and rapid handling of submitted and invited papers. They seek qualified reviewers and make editorial decisions based on their own judgments as informed by the reviews.Members of the Editorial Board are carefully chosen by the Associate Editors and the Editor-in-Chief based on expertise in their field, as well as their reviewer and publishing history. The process of choosing and inviting editors, which this year was accomplished with the help of incoming Editor-in-Chief Jane Dyson, is always gratifying. I am proud that BJ will be led by such an outstanding new class of editors, who will join the eminent and dedicated scientists with continuing terms. Editors are chosen not only for their innovative science but also to span the diversity of biophysics. Another important criterion was that they have demonstrated their commitment to rapid and rigorous peer review, often as frequent reviewers for BJ. As authors, reviewers, and readers, we owe the excellence that we all expect from BJ to the generous service offered by these committed volunteers.One notable change this year is that Elizabeth Rhoades will move into the Associate Editor position for Section II, Proteins. The Section has been expertly led by Nathan Baker, who will continue on as an Editorial Board Member. We thank all of the new members in the class of 2019 for agreeing to serve. We also extend a large thank you to the 20 editors who have fulfilled their terms in 2016 and are rotating off the Editorial Board.A list of all 130 BJ Editorial Board members is available through the journal webpage at http://www.cell.com/biophysj/editorial-board. The incoming class of editors includes:Section 1 – Nucleic Acids and Genome BiophysicsDavid LilleyGijs WuiteSection II - ProteinsMadan BabuMartin BuehlerMonika FuxreiterWendy ShawSection III – Channels and TransportersBaron ChandaChris ChipotMichael GrabeSection IV - MembranesMichael BrownCharles DeberTommy NylanderDimitrious StamouPeter TielmanJoe ZasadzinskiSection V – Molecular Machines, Motors, and Nanoscale BiophysicsSteven RosenfeldSection VI – Cell BiophysicsKinneret KerenJoachim MuellerAmy PalmerJason SwedlowSection VII – Systems BiophysicsMark AlberVivek ShenoyArthur ShermanRaimond WinslowIn addition to the new Editorial Board, 2017 brings with it new developments for Biophysical Journal.The journal is pleased to announce that the length requirement for Letters has been extended from three to five printed pages (including figures and references). In addition, because the Letter article type is intended for especially urgent and exciting research, they will be placed on a special rapid review track and will be published online ahead of print, in addition to appearing in the next issue of the Journal. Finally, Letters no longer need to be submitted using a template. To see the change in fee structure for Letters, please refer to the newly revised Guidelines for Authors.In an exciting development this past year, BJ began accepting manuscript submissions directly from the preprint server bioRxiv. The journal also continues to welcome submissions that had been previously deposited in arXiv. Now, to document and help readers trace the complete publication record, authors are invited to voluntarily provide a footnote for their BJ article referencing their preprint in bioRxiv or arXiv, including the DOI number and the date the initial manuscript was deposited.Biophysical Journal authors can now submit multidimensional time series data, such as 3D multichannel time series from live cell microscopy experiments. Readers can view this data with an interactive viewer called Virtual Microscope, permitting them to scroll through multiple channel z-stacks at a given time point or through time at a selected z-slice. Instructions for submitting these files will be provided during the decision cycle.Readers can expect several special issues on important topics in the coming year: “Genome Biophysics”; “Liposomes, Exosomes, Virosomes: From Modeling Complex Membrane Processes to Medical Diagnostics and Drug Delivery”; “Mechanobiology”; “Challenges in RNA Modeling and Design”; and “Brain Biophysics”. Several of these still have open calls for papers with closing dates that can be found through the BJ website. The journal also will soon be releasing a new article collection on single-molecule biophysics.Finally, in the first half of 2017 the journal will move to a mobile-responsive format to provide an optimized reading experience for all users. You will see some improvements to the home page as well as to the online article format.Make a New Year’s resolution to send your best research to Biophysical Journal in 2017!

Cell viscoelastic properties are affected by the cell cycle, differentiation, and pathological processes such as malignant transformation. Therefore, evaluation of the mechanical properties of the cells proved to be an approach to obtaining information on the functional state of the cells. Most of the currently used methods for cell mechanophenotyping are limited by low robustness or the need for highly expert operation. In this paper, the system and method for viscoelasticity measurement using shear stress induction by fluid flow is described and tested. Quantitative phase imaging (QPI) is used for image acquisition because this technique enables one to quantify optical path length delays introduced by the sample, thus providing a label-free objective measure of morphology and dynamics. Viscosity and elasticity determination were refined using a new approach based on the linear system model and parametric deconvolution. The proposed method allows high-throughput measurements during live-cell experiments and even through a time lapse, whereby we demonstrated the possibility of simultaneous extraction of shear modulus, viscosity, cell morphology, and QPI-derived cell parameters such as circularity or cell mass. Additionally, the proposed method provides a simple approach to measure cell refractive index with the same setup, which is required for reliable cell height measurement with QPI, an essential parameter for viscoelasticity calculation. Reliability of the proposed viscoelasticity measurement system was tested in several experiments including cell types of different Young/shear modulus and treatment with cytochalasin D or docetaxel, and an agreement with atomic force microscopy was observed. The applicability of the proposed approach was also confirmed by a time-lapse experiment with cytochalasin D washout, whereby an increase of stiffness corresponded to actin repolymerization in time.

FiberSim is a flexible open-source model of myofilament-level contraction. The code uses a spatially explicit technique, meaning that it tracks the position and status of each contractile molecule within the lattice framework. This allows the model to simulate some of the mechanical effects modulated by myosin-binding protein C, as well as the dose dependence of myotropes and the effects of varying isoform expression levels. This paper provides a short introduction to FiberSim and presents simulations of tension-pCa curves with and without regulation of thick and thin filament activation by myosin-binding protein C. A myotrope dose-dependent response as well as slack/re-stretch maneuvers to assess rates of tension recovery are also presented. The software was designed to be flexible (the user can define their own model and/or protocol) and computationally efficient (simulations can be performed on a regular laptop). We hope that other investigators will use FiberSim to explore myofilament level mechanisms and to accelerate research focusing on the contractile properties of sarcomeres.

This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy).This article has been retracted at the request of Edward Egelman, Editor-in-Chief.The editors have noted that there is a substantial overlap of figures and text between this Biophysical Journal article and D. Rutkauskas, V. Novoderezkhin, R.J. Cogdell and R. van Grondelle. Fluorescence spectral fluctuations of single LH2 complexes from Rhodopseudomonas acidophila strain 10050. Biochemistry, 43 (2004) 4431–4438, doi:10.1021/bi0497648. The submission of this paper was inconsistent with the Biophysical Journal policy which states: “Manuscripts submitted to Biophysical Journal (BJ) must be original; papers that have already been published or are concurrently submitted elsewhere for publication are not acceptable for submission. This includes manuscripts previously submitted to BJ, as well as material that has been submitted to other journals while BJ is considering the manuscript. If some part of the work has appeared or will appear elsewhere, the authors must give the specific details of such appearances in the cover letter accompanying the BJ submission. If previously published illustrative material, such as figures or tables, must be included, the authors are responsible for obtaining the appropriate permissions from the publisher(s) before the material may be published in BJ”. We are therefore retracting the publication of the Biophysical Journal article.

The Biophysical Journal is committed to rigorous and fair peer review. Peer review serves our authors by helping them improve their research and how it is presented. Peer review serves our scientific community by assuring that the papers published in the Biophysical Journal have been carefully evaluated for both technical validity and scientific significance. Finally, prepublication peer review serves the general societal good by helping guard against bad science, which could lead to poor or even dangerous public policy. Indeed, in this age of rapid dissemination of both facts and fiction, publishing bad science actually provides cover to the enemies of rational science-based decision making (e.g., the politicization of climate change or the myth of an association between childhood vaccination and autism).But why am I writing an editorial about an idea that should be so self-evident and has been a bedrock of the scientific enterprise for 200 years? Unfortunately, the value of prepublication peer review has been questioned recently in very provocative blogs, tweets, and editorials, often by prominent scientists. The primary argument against peer review is that it may delay the dissemination of important science and that it can be capricious. But the attack is also often promoted by publishers of an expanding list of new journals advocating “postpublication peer review.” These are driven to publish as many papers as possible, because their business models rely on a high number of contributing authors and/or a large volume of published articles.I am proud of Biophysical Journal’s fair and thorough review process, which is overseen by an outstanding Editorial Board composed of working scientists rather than professional editors. We also pride ourselves on the speed of our review process. Of course, peer review is not perfect. We simply cannot guarantee that every single decision will be completely fair and quick. But it is the best system we have to assure that published science is valid, replicable, and important. It is also the best system to deter political agenda-driven or snake oil “science.”But is there more that the biophysics community and Biophysical Journal can do to promote the rapid and free exchange of ideas prior to peer review? We can certainly learn from the successful track record of the arXiv (https://arxiv.org/) preprint server, which has established itself over the last 25 years as a valued medium for the dissemination of ideas and results in the physics community. Indeed, Biophysical Journal has long had the policy of accepting submission of papers that had been previously deposited in arXiv. Recently, we enhanced the Biophysical Journal submission site so authors of articles posted on arXiv may enter their article ID number to autopopulate their submission to Biophysical Journal with the appropriate metadata for that paper. However, not all papers produced by the biophysics community are appropriate for arXiv, and even those that are deposited there may not be noticed by scientists who are more focused on biology.For these reasons, we have welcomed the new bioRxiv (http://biorxiv.org/) repository established by Cold Spring Harbor Laboratory (CSHL). Indeed, in January of this year, Biophysical Journal was among the first pilot group of six journals that enabled direct submission of papers from the bioRxiv website. After depositing your paper on bioRxiv, you may click a button to automatically submit the paper to Biophysical Journal. CSHL is, of course, a venerable not-for-profit research institute. They have offered bioRxiv as a free service to the life sciences research community.Deposition of manuscripts in bioRxiv (or arXiv) eliminates the concern that the peer review process can be long and capricious; research is available to the world within a day of submission for all to study, praise, or criticize. In fact, deposition on preprint servers has the collateral benefit of providing immediate and permanent open access to research results. There are some scientists who might worry that their ideas will be stolen if circulated prematurely in this manner. But the long track record of arXiv demonstrates this is not generally a concern; indeed, I see no reason why the date of preprint submission shouldn’t serve as evidence of priority after a paper is ultimately published in a peer reviewed journal. For these reasons, I intend to deposit papers from my own lab in bioRxiv and have recently completed my first pleasant experience doing so.But, at the same time, the value of blind peer review should not be compromised. I believe that only peer-reviewed work should be considered in personnel decisions and grant reviews. Any relaxation of this standard would lead to chaos. Also, bioRxiv will need to carefully consider the societal impact of papers they expose to the public. The potential for danger in this regard will be stronger for bioRxiv than it has been for arXiv. As an extreme example, drug trials should simply never be published without rigorous peer review. But there may also be more subtle problems. A study claiming a link between cell phone use and brain cancer (http://biorxiv.org/content/early/2016/06/23/055699) appeared recently in bioRxiv and was widely reported in the lay press and social media, despite clear shortcomings. Thankfully, some experienced science writers recognized that the work was not peer reviewed and that it followed on a long history of previously debunked claims of this sort. So, after the initial flurry, there was a quick series of articles and blogs critical of the study (e.g., the thoughtful piece by Aaron E. Carroll in the New York Times: “Why It’s Not Time to Panic About Cellphones and Cancer”; http://www.nytimes.com/2016/06/02/upshot/why-its-not-time-to-panic-about-cellphones-and-cancer.html?smid=tw-share&_r=1). On the one hand, it is reassuring that the lay press ultimately got this story right. But it also raises questions. How many people were influenced by the initial news of this study, never seeing any of the later skeptical articles? How would a preprint with similar sensational public health implications, but without the history of previous bad science, be reported by the mainstream media? I urge the publishers and Advisory Board of bioRxiv at CSHL to consider these issues and develop policies to deal with them. I also applaud them for undertaking this bold and noble initiative to serve the life science research community.

Antimicrobial peptides have two binding states in a lipid bilayer, a surface state S and a pore-forming state I. The transition from the S state to the I state has a sigmoidal peptide-concentration dependence indicating cooperativity in the peptide-membrane interactions. In a previous paper, we reported the transition of alamethicin measured in three bilayer conditions. The data were explained by a free energy that took into account the membrane thinning effect induced by the peptides. In this paper, the full implications of the free energy were tested by including another type of peptide, melittin, that forms toroidal pores, instead of barrel-stave pores as in the case of alamethicin. The S-to-I transitions were measured by oriented circular dichroism. The membrane thinning effect was measured by x-ray diffraction. All data were in good agreement with the theory, indicating that the membrane thinning effect is a plausible mechanism for the peptide-induced pore formations.

Ion channels catalyze the transport of ions across biological membranes. A proper understanding of ion-channel functioning is essential to our knowledge of cell physiology, and, in this context, ion-channel selectivity is a key concept. The extent to which a channel permeates two ion species, a and b, is expressed by the permeability ratio, P a / P b . This paper addresses a complication in the calculation of P a / P b that is related to the existence of surface potentials ( ψ ) and that so far has not been fully appreciated. This paper shows the rather surprising effect of ψ on the calculated P a /P b of a channel that is permeable to two ion species of different valence. If we ignore ψ , we conclude, for instance, P a > P b . If we implement ψ in the calculation of P a / P b , we may, however, conclude exactly the reverse, i.e., P a P b . Because electrostatic potentials arise at the surface of essentially all biological membranes, this paper argues for a more critical evaluation of ion channel selectivity measurements.

In this paper, we consider the implications of the general theory developed in the accompanying paper, to interpret experiments on DNA overstretching that involve variables such as solution temperature, pH, and ionic strength. We find the DNA helix-coil phase boundary in the force-temperature space. At temperatures significantly below the regular (zero force) DNA melting temperature, the overstretching force, f ov ( T ) , is predicted to decrease nearly linearly with temperature. We calculate the slope of this dependence as a function of entropy and heat-capacity changes upon DNA melting. Fitting of the experimental f ov ( T ) dependence allows determination of both of these quantities in very good agreement with their calorimetric values. At temperatures slightly above the regular DNA melting temperature, we predict stabilization of dsDNA by moderate forces, and destabilization by higher forces. Thus the DNA stretching curves, f ( b ) , should exhibit two rather than one overstretching transitions: from single stranded (ss) to double stranded (ds) and then back at the higher force. We also predict that any change in DNA solution conditions that affects its melting temperature should have a similar effect on DNA overstretching force. This result is used to calculate the dependence of DNA overstretching force on solution pH, f ov (pH), from the known dependence of DNA melting temperature on pH. The calculated f ov (pH) is in excellent agreement with its experimental determination (M. C. Williams, J. R. Wenner, I. Rouzina, and V. A. Bloomfield, Biophys. J. , accepted for publication). Finally, we quantitatively explain the measured dependence of DNA overstretching force on solution ionic strength for crosslinked and noncrosslinked DNA. The much stronger salt dependence of f ov in noncrosslinked DNA results from its lower linear charge density in the melted state, compared to crosslinked or double-stranded overstretched S-DNA.

Proteins must be stable to accomplish their biological function and to avoid enzymatic degradation. Constitutive proteolysis, however, is the main source of free amino acids used for de novo protein synthesis. In this paper the delicate balance of protein stability and degradability is discussed in the context of function of major histocompatibility complex (MHC) encoded protein. Classical MHC proteins are single-use peptide transporters that carry proteolytic degradation products to the cell surface for presenting them to T cells. These proteins fulfill their function as long as they bind their dissociable ligand, the peptide. Ligand-free MHC molecules on the cell surface are practically useless for their primary biological function, but may acquire novel activity or become an important source of amino acids when they lose their compact stable structure, which resists proteolytic attacks. We show in this paper that one or more of the stabilization centers responsible for the stability of MHC-peptide complexes is composed of residues of both the protein and the peptide, therefore missing in the ligand-free protein. This arrangement of stabilization centers provides a simple means of regulation; it makes the useful form of the protein stable, whereas the useless form of the same protein is unstable and therefore degradable.

Membrane proteins often cluster in nanoscale membrane domains (lipid rafts) that coalesce into ceramide-rich platforms during cell stress, however the clustering mechanisms remain uncertain. The cystic fibrosis transmembrane conductance regulator (CFTR), which is mutated in cystic fibrosis (CF), forms clusters that are cholesterol dependent and become incorporated into long-lived platforms during hormonal stimulation. We report here that clustering does not involve known tethering interactions of CFTR with PDZ domain proteins, filamin A or the actin cytoskeleton. It also does not require CFTR palmitoylation but is critically dependent on membrane lipid order and is induced by detergents that increase the phase separation of membrane lipids. Clustering and integration of CFTR into ceramide-rich platforms are abolished by the disease mutations F508del and S13F and rescued by the CFTR modulators elexacaftor plus tezacaftor. These results indicate CF therapeutics that correct mutant protein folding restore both trafficking and normal lipid interactions in the plasma membrane. This article has an associated First Person interview with the first author of the paper.

Biomolecular condensates have been shown to play a fundamental role in localizing biochemistry in a cell. RNA is a common constituent of condensates, and can determine their biophysical properties. Functions of biomolecular condensates are varied including activating, inhibiting, and localizing reactions. Recent theoretical work has shown that the phase separation of proteins into droplets can diminish cell to cell variability in protein abundance. However, the extent to which phase separation involving mRNAs may also buffer noise has yet to be explored. In this paper, we introduce a phenomenological model for the phase separation of mRNAs into RNP condensates, and quantify noise suppression as a function of gene expression kinetic parameters. Through stochastic simulations, we highlight the ability for condensates formed from just a handful of mRNAs to regulate the abundance and suppress the fluctuations of proteins. We place particular emphasis on how this mechanism can facilitate efficient transcription by reducing noise even in the situation of infrequent bursts of transcription by exploiting the physics of a concentration-dependent, deterministic phase separation threshold. We investigate two biologically relevant models in which phase separation acts to either "buffer" noise by storing mRNA in inert droplets, or "filter" phase separated mRNAs by accelerating their decay, and quantify expression noise as a function of kinetic parameters. In either case the most efficient expression occurs when bursts produce mRNAs close the phase separation threshold, which we find to be broadly consistent with observations of an RNP-droplet forming cyclinin multinucleate Ashbya gossypii cells. We finally consider the contribution of noise in the phase separation threshold, and show that protein copy number noise can be suppressed by phase separation threshold fluctuations in certain conditions.