A Molecular Grammar Governing the Driving Forces for Phase Separation of Prion-like RNA Binding Proteins.

Proteins such as FUS phase separate to form liquid-like condensates that can harden into less dynamic structures. However, how these properties emerge from the collective interactions of many amino acids remains largely unknown. Here, we use extensive mutagenesis to identify a sequence-encoded molecular grammar underlying the driving forces of phase separation of proteins in the FUS family and test aspects of this grammar in cells. Phase separation is primarily governed by multivalent interactions among tyrosine residues from prion-like domains and arginine residues from RNA-binding domains, which are modulated by negatively charged residues. Glycine residues enhance the fluidity, whereas glutamine and serine residues promote hardening. We develop a model to show that the measured saturation concentrations of phase separation are inversely proportional to the product of the numbers of arginine and tyrosine residues. These results suggest it is possible to predict phase-separation properties based on amino acid sequences.

Low-Affinity Binding Sites and the Transcription Factor Specificity Paradox in Eukaryotes.

Eukaryotic transcription factors (TFs) from the same structural family tend to bind similar DNA sequences, despite the ability of these TFs to execute distinct functions in vivo. The cell partly resolves this specificity paradox through combinatorial strategies and the use of low-affinity binding sites, which are better able to distinguish between similar TFs. However, because these sites have low affinity, it is challenging to understand how TFs recognize them in vivo. Here, we summarize recent findings and technological advancements that allow for the quantification and mechanistic interpretation of TF recognition across a wide range of affinities. We propose a model that integrates insights from the fields of genetics and cell biology to provide further conceptual understanding of TF binding specificity. We argue that in eukaryotes, target specificity is driven by an inhomogeneous 3D nuclear distribution of TFs and by variation in DNA binding affinity such that locally elevated TF concentration allows low-affinity binding sites to be functional.

A conceptual framework for understanding phase separation and addressing open questions and challenges.

Macromolecular phase separation is being recognized for its potential importance and relevance as a driver of spatial organization within cells. Here, we describe a framework based on synergies between networking (percolation or gelation) and density (phase separation) transitions. Accordingly, the phase transitions in question are referred to as phase separation coupled to percolation (PSCP). The condensates that result from PSCP are viscoelastic network fluids. Such systems have sequence-, composition-, and topology-specific internal network structures that give rise to time-dependent interplays between viscous and elastic properties. Unlike pure phase separation, the process of PSCP gives rise to sequence-, chemistry-, and structure-specific distributions of clusters that can form at concentrations that lie well below the threshold concentration for phase separation. PSCP, influenced by specific versus solubility-determining interactions, also provides a bridge between different observations and helps answer questions and address challenges that have arisen regarding the role of macromolecular phase separation in biology.

Biotechnological perspective for wireless energy: H2-based power extraction from air.

Despite its extreme scarcity, atmospheric H2 serves as an energy source for some prokaryotes. Recently, Grinter, Kropp, et al. reported the structural, biochemical, electrochemical, and spectroscopic elucidation of an underlying H2 catalyst, a [NiFe]-hydrogenase, which, owing to its extremely high affinity, facilitates the extraction of energy from ambient air.

Small and Large Ribosomal Subunit Deficiencies Lead to Distinct Gene Expression Signatures that Reflect Cellular Growth Rate.

Levels of the ribosome, the conserved molecular machine that mediates translation, are tightly linked to cellular growth rate. In humans, ribosomopathies are diseases associated with cell-type-specific pathologies and reduced ribosomal protein (RP) levels. Because gene expression defects resulting from ribosome deficiency have not yet been experimentally defined, we systematically probed mRNA, translation, and protein signatures that were either unlinked from or linked to cellular growth rate in RP-deficient yeast cells. Ribosome deficiency was associated with altered translation of gene subclasses, and profound general secondary effects of RP loss on the spectrum of cellular mRNAs were seen. Among these effects, growth-defective 60S mutants increased synthesis of proteins involved in proteasome-mediated degradation, whereas 40S mutants accumulated mature 60S subunits and increased translation of ribosome biogenesis genes. These distinct signatures of protein synthesis suggest intriguing and currently mysterious differences in the cellular consequences of deficiency for small and large ribosomal subunits.

Ribosome biogenesis and function in development and disease.

Although differential transcription drives the development of multicellular organisms, the ultimate readout of a protein-coding gene is ribosome-dependent mRNA translation. Ribosomes were once thought of as uniform molecular machines, but emerging evidence indicates that the complexity and diversity of ribosome biogenesis and function should be given a fresh look in the context of development. This Review begins with a discussion of different developmental disorders that have been linked with perturbations in ribosome production and function. We then highlight recent studies that reveal how different cells and tissues exhibit variable levels of ribosome production and protein synthesis, and how changes in protein synthesis capacity can influence specific cell fate decisions. We finish by touching upon ribosome heterogeneity in stress responses and development. These discussions highlight the importance of considering both ribosome levels and functional specialization in the context of development and disease.

Preexisting social ties among Auschwitz prisoners support Holocaust survival.

Survivor testimonies link survival in deadly POW camps, Gulags, and Nazi concentration camps to the formation of close friendships with other prisoners. To provide evidence free of survival bias on the importance of social ties for surviving the Holocaust, we study individual histories of 30 thousand Jewish prisoners who entered the Auschwitz-Birkenau concentration camp on transports from the Theresienstadt ghetto. We ask whether the availability of potential friends among fellow prisoners on a transport influenced the chances of surviving the Holocaust. Relying on multiple proxies of preexisting social networks and varying social-linkage composition of transports, we uncover a significant survival advantage to entering Auschwitz with a larger group of potential friends.

Microbial population dynamics decouple growth response from environmental nutrient concentration.

How the growth rate of a microbial population responds to the environmental availability of chemical nutrients and other resources is a fundamental question in microbiology. Models of this response, such as the widely used Monod model, are generally characterized by a maximum growth rate and a half-saturation concentration of the resource. What values should we expect for these half-saturation concentrations, and how should they depend on the environmental concentration of the resource? We survey growth response data across a wide range of organisms and resources. We find that the half-saturation concentrations vary across orders of magnitude, even for the same organism and resource. To explain this variation, we develop an evolutionary model to show that demographic fluctuations (genetic drift) can constrain the adaptation of half-saturation concentrations. We find that this effect fundamentally differs depending on the type of population dynamics: Populations undergoing periodic bottlenecks of fixed size will adapt their half-saturation concentrations in proportion to the environmental resource concentrations, but populations undergoing periodic dilutions of fixed size will evolve half-saturation concentrations that are largely decoupled from the environmental concentrations. Our model not only provides testable predictions for laboratory evolution experiments, but it also reveals how an evolved half-saturation concentration may not reflect the organism's environment. In particular, this explains how organisms in resource-rich environments can still evolve fast growth at low resource concentrations. Altogether, our results demonstrate the critical role of population dynamics in shaping fundamental ecological traits.

Tough and fatigue-resistant polymer networks by crack tip softening.

Soft materials fail by crack propagation under external loads. While fracture toughness of a soft material can be enhanced by orders of magnitude, its fatigue threshold remains insusceptible. In this work, we demonstrate a crack tip softening (CTS) concept to simultaneously improve the toughness and threshold of a single polymeric network. Polyacrylamide hydrogels have been selected as a model material. The polymer network is cured by two kinds of crosslinkers: a normal crosslinker and a light-degradable crosslinker. We characterize the pristine sample and light-treated sample by shear modulus, fracture toughness, fatigue threshold, and fractocohesive length. Notably, we apply light at the crack tip of a sample so that the light-sensitive crosslinkers degrade, resulting in a CTS sample with a softer and elastic crack tip. The pristine sample has a fracture toughness of 748.3 ± 15.19 J/m2 and a fatigue threshold of 9.3 J/m2. By comparison, the CTS sample has a fracture toughness of 2,774.6 ± 127.14 J/m2 and a fatigue threshold of 33.8 J/m2. Both fracture toughness and fatigue threshold have been enhanced by about four times. We attribute this simultaneous enhancement to stress de-concentration and elastic shielding at the crack tip. Different from the "fiber/matrix composite" concept and the "crystallization at the crack tip" concept, the CTS concept in the present work provides another option to simultaneously enhance the toughness and threshold, which improves the reliability of soft devices during applications.

Charge transfer as a mechanism for chlorophyll fluorescence concentration quenching.

Highly concentrated solutions of chlorophyll display rapid fluorescence quenching. The same devastating energy loss is not seen in photosynthetic light-harvesting antenna complexes, despite the need for chromophores to be in close proximity to facilitate energy transfer. A promising, though unconfirmed mechanism for the observed quenching is energy transfer from an excited chlorophyll monomer to a closely associated chlorophyll pair that subsequently undergoes rapid nonradiative decay to the ground state via a short-lived intermediate charge-transfer state. In this work, we make use of newly emerging fast methods in quantum chemistry to assess the feasibility of this proposed mechanism. We calculate rate constants for the initial charge separation, based on Marcus free-energy surfaces extracted from molecular dynamics simulations of solvated chlorophyll pairs, demonstrating that this pathway will compete with fluorescence (i.e., drive quenching) at experimentally measured quenching concentrations. We show that the rate of charge separation is highly sensitive to interchlorophyll distance and the relative orientations of chromophores within a quenching pair. We discuss possible solvent effects on the rate of charge separation (and consequently the degree of quenching), using the light-harvesting complex II (LH2) protein from rps. acidophila as a specific example of how this process might be controlled in a protein environment. Crucially, we reveal that the LH2 antenna protein prevents quenching, even at the high chlorophyll concentrations required for efficient energy transfer, by restricting the range of orientations that neighboring chlorophyll pairs can adopt.

Tradeoffs in bacterial physiology determine the efficiency of antibiotic killing.

Antibiotic effectiveness depends on a variety of factors. While many mechanistic details of antibiotic action are known, the connection between death rate and bacterial physiology is poorly understood. A common observation is that death rate in antibiotics rises linearly with growth rate; however, it remains unclear how other factors, such as environmental conditions and whole-cell physiological properties, affect bactericidal activity. To address this, we developed a high-throughput assay to precisely measure antibiotic-mediated death. We found that death rate is linear in growth rate, but the slope depends on environmental conditions. Growth under stress lowers death rate compared to nonstressed environments with similar growth rate. To understand stress's role, we developed a mathematical model of bacterial death based on resource allocation that includes a stress-response sector; we identify this sector using RNA-seq. Our model accurately predicts the minimal inhibitory concentration (MIC) with zero free parameters across a wide range of growth conditions. The model also quantitatively predicts death and MIC when sectors are experimentally modulated using cyclic adenosine monophosphate (cAMP), including protection from death at very low cAMP levels. The present study shows that different conditions with equal growth rate can have different death rates and establishes a quantitative relation between growth, death, and MIC that suggests approaches to improve antibiotic efficacy.

Revealing the missing puzzle piece of concentration in regulating Zn electrodeposition.

Despite achievements in suppressing dendrites and regulating Zn crystal growth, secondary aqueous Zn batteries are still rare in the market. Existing strategies mainly focus on electrode modification and electrolyte optimization, while the essential role of ion concentration in liquid-to-solid electrodeposition is neglected for a long time. Herein, the mechanism of concentration regulation in Zn electrodeposition is investigated in depth by combining electrochemical tests, post hoc characterization, and multiscale simulations. First, initial Zn electrodeposition is thermodynamically controlled epitaxial growth, whereas with the rapid depletion of ions, the concentration overpotential transcends the thermodynamic influence to kinetic control. Then, the evolution of the morphology from 2D sheets to 1D whiskers due to the concentration change is insightfully revealed by the morphological characterization and phase-field modeling. Furthermore, the depth of discharge (DOD) results in large concentration differences at the electrode-electrolyte interface, with a mild concentration distribution at lower DOD generating (002) crystal plane 2D sheets and a heavily varied concentration distribution at higher DOD yielding arbitrarily oriented 3D blocks. As a proof of concept, relaxation is introduced into two systems to homogenize the concentration distribution, revalidating the essential role of concentration in regulating electrodeposition, and two vital factors affecting the relaxation time, i.e., current density and electrode distance, are deeply investigated, demonstrating that the relaxation time is positively related to both and is more sensitive to the electrode distance. This work contributes to reacquainting aqueous batteries undergoing phase transitions and reveals a missing piece of the puzzle in regulating Zn electrodeposition.

Free-standing membrane incorporating single-atom catalysts for ultrafast electroreduction of low-concentration nitrate.

The release of wastewaters containing relatively low levels of nitrate (NO3-) results in sufficient contamination to induce harmful algal blooms and to elevate drinking water NO3- concentrations to potentially hazardous levels. In particular, the facile triggering of algal blooms by ultra-low concentrations of NO3- necessitates the development of efficient methods for NO3- destruction. However, promising electrochemical methods suffer from weak mass transport under low reactant concentrations, resulting in long treatment times (on the order of hours) for complete NO3- destruction. In this study, we present flow-through electrofiltration via an electrified membrane incorporating nonprecious metal single-atom catalysts for NO3- reduction activity enhancement and selectivity modification, achieving near-complete removal of ultra-low concentration NO3- (10 mg-N L-1) with a residence time of only a few seconds (10 s). By anchoring Cu single atoms supported on N-doped carbon in a carbon nanotube interwoven framework, we fabricate a free-standing carbonaceous membrane featuring high conductivity, permeability, and flexibility. The membrane achieves over 97% NO3- removal with high N2 selectivity of 86% in a single-pass electrofiltration, which is a significant improvement over flow-by operation (30% NO3- removal with 7% N2 selectivity). This high NO3- reduction performance is attributed to the greater adsorption and transport of nitric oxide under high molecular collision frequency coupled with a balanced supply of atomic hydrogen through H2 dissociation during electrofiltration. Overall, our findings provide a paradigm of applying a flow-through electrified membrane incorporating single-atom catalysts to improve the rate and selectivity of NO3- reduction for efficient water purification.

Prediction of transcript structure and concentration using RNA-Seq data.

Alternative splicing (AS) is a key post-transcriptional modification that helps in increasing protein diversity. Almost 90% of the protein-coding genes in humans are known to undergo AS and code for different transcripts. Some transcripts are associated with diseases such as breast cancer, lung cancer and glioblastoma. Hence, these transcripts can serve as novel therapeutic and prognostic targets for drug discovery. Herein, we have developed a pipeline, Finding Alternative Splicing Events (FASE), as the R package that includes modules to determine the structure and concentration of transcripts using differential AS. To predict the correct structure of expressed transcripts in given conditions, FASE combines the AS events with the information of exons, introns and junctions using graph theory. The estimated concentration of predicted transcripts is reported as the relative expression in terms of log2CPM. Using FASE, we were able to identify several unique transcripts of EMILIN1 and SLK genes in the TCGA-BRCA data, which were validated using RT-PCR. The experimental study demonstrated consistent results, which signify the high accuracy and precision of the developed methods. In conclusion, the developed pipeline, FASE, can efficiently predict novel transcripts that are missed in general transcript-level differential expression analysis. It can be applied selectively from a single gene to simple or complex genome even in multiple experimental conditions for the identification of differential AS-based biomarkers, prognostic targets and novel therapeutics.

Electrochemical modulation enhances the selectivity of peripheral neurostimulation in vivo.

Electrical nerve stimulation serves an expanding list of clinical applications, but it faces persistent challenges in selectively activating bundled nerve fibers. In this study, we investigated electrochemical modulation with an ion-selective membrane (ISM) and whether it, used together with electrical stimulation, may provide an approach for selective control of peripheral nerves. Guided by theoretical transport modeling and direct concentration measurements, we developed an implantable, multimodal ISM cuff capable of simultaneous electrical stimulation and focused Ca2+ depletion. Acutely implanting it on the sciatic nerve of a rat in vivo, we demonstrated that Ca2+ depletion could increase the sensitivity of the nerve to electrical stimulation. Furthermore, we found evidence that the effect of ion modulation would selectively influence functional components of the nerve, allowing selective activation by electrical current. Our results raise possibilities for improving functional selectivity of new and existing bioelectronic therapies, such as vagus nerve stimulation.

Concentration gradients in evaporating binary droplets probed by spatially resolved Raman and NMR spectroscopy.

Understanding the evaporation process of binary sessile droplets is essential for optimizing various technical processes, such as inkjet printing or heat transfer. Liquid mixtures whose evaporation and wetting properties may differ significantly from those of pure liquids are particularly interesting. Concentration gradients may occur in these binary droplets. The challenge is to measure concentration gradients without affecting the evaporation process. Here, spectroscopic methods with spatial resolution can discriminate between the components of a liquid mixture. We show that confocal Raman microscopy and spatially resolved NMR spectroscopy can be used as complementary methods to measure concentration gradients in evaporating 1-butanol/1-hexanol droplets on a hydrophobic surface. Deuterating one of the liquids allows analysis of the local composition through the comparison of the intensities of the C­H and C­D stretching bands in Raman spectra. Thus, a concentration gradient in the evaporating droplet was established. Spatially resolved NMR spectroscopy revealed the composition at different positions of a droplet evaporating in the NMR tube, an environment in which air exchange is less pronounced. While not being perfectly comparable, both methods­confocal Raman and spatially resolved NMR experiments­show the presence of a vertical concentration gradient as 1-butanol/1-hexanol droplets evaporate.

LRBA is essential for urinary concentration and body water homeostasis.

Protein kinase A (PKA) directly phosphorylates aquaporin-2 (AQP2) water channels in renal collecting ducts to reabsorb water from urine for the maintenance of systemic water homeostasis. More than 50 functionally distinct PKA-anchoring proteins (AKAPs) respectively create compartmentalized PKA signaling to determine the substrate specificity of PKA. Identification of an AKAP responsible for AQP2 phosphorylation is an essential step toward elucidating the molecular mechanisms of urinary concentration. PKA activation by several compounds is a novel screening strategy to uncover PKA substrates whose phosphorylation levels were nearly perfectly correlated with that of AQP2. The leading candidate in this assay proved to be an AKAP termed lipopolysaccharide-responsive and beige-like anchor protein (LRBA). We found that LRBA colocalized with AQP2 in vivo, and Lrba knockout mice displayed a polyuric phenotype with severely impaired AQP2 phosphorylation. Most of the PKA substrates other than AQP2 were adequately phosphorylated by PKA in the absence of LRBA, demonstrating that LRBA-anchored PKA preferentially phosphorylated AQP2 in renal collecting ducts. Furthermore, the LRBA-PKA interaction, rather than other AKAP-PKA interactions, was robustly dissociated by PKA activation. AKAP-PKA interaction inhibitors have attracted attention for their ability to directly phosphorylate AQP2. Therefore, the LRBA-PKA interaction is a promising drug target for the development of anti-aquaretics.

Aerosol particle emission increases exponentially above moderate exercise intensity resulting in superemission during maximal exercise.

Many airborne pathogens such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are transmitted indoors via aerosol particles. During exercise, pulmonary ventilation can increase over 10-fold, and therefore, exercisers will exhale a greater volume of aerosol-containing air. However, we currently do not know how exercise affects the concentration of aerosol particles in exhaled air and the overall emission of aerosol particles. Consequently, we developed a method to measure in parallel the concentration of aerosol particles in expired air, pulmonary ventilation, and aerosol particle emission at rest and during a graded exercise test to exhaustion. We used this method to test eight women and eight men in a descriptive study. We found that the aerosol particle concentration in expired air increased significantly from 56 ± 53 particles/liter at rest to 633 ± 422 particles/liter at maximal intensity. Aerosol particle emission per subject increased significantly by a factor of 132 from 580 ± 489 particles/min at rest to a super emission of 76,200 ± 48,000 particles/min during maximal exercise. There were no sex differences in aerosol particle emission, but endurance-training subjects emitted significantly more aerosol particles during maximal exercise than untrained subjects. Overall, aerosol particle emission increased moderately up to an exercise intensity of ∼2 W/kg and exponentially thereafter. Together, these data might partly explain superspreader events especially during high-intensity group exercise indoors and suggest that strong infection prevention measures are needed especially during exercise at an intensity that exceeds ∼2 W/kg. Investigations of influencing factors like airway and whole-body hydration status during exercise on aerosol particle generation are needed.

Hydrodynamic flow and concentration gradients in the gut enhance neutral bacterial diversity.

The gut microbiota features important genetic diversity, and the specific spatial features of the gut may shape evolution within this environment. We investigate the fixation probability of neutral bacterial mutants within a minimal model of the gut that includes hydrodynamic flow and resulting gradients of food and bacterial concentrations. We find that this fixation probability is substantially increased, compared with an equivalent well-mixed system, in the regime where the profiles of food and bacterial concentration are strongly spatially dependent. Fixation probability then becomes independent of total population size. We show that our results can be rationalized by introducing an active population, which consists of those bacteria that are actively consuming food and dividing. The active population size yields an effective population size for neutral mutant fixation probability in the gut.

Chaperone Machineries of Rubisco - The Most Abundant Enzyme.

A major challenge faced by human civilization is to ensure that agricultural productivity keeps pace with population growth and a changing climate. All food supply is generated, directly or indirectly, through the process of photosynthesis, with the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyzing the assimilation of atmospheric CO2. Despite its pivotal role, Rubisco is a remarkably inefficient enzyme and must be made by plants in large quantities. However, efforts to enhance Rubisco performance by bioengineering have been hampered by its extensive reliance on molecular chaperones and auxiliary factors for biogenesis, metabolic repair, and packaging into membraneless microcompartments. Here, we review recent advances in understanding these complex machineries and discuss their implications for improving Rubisco carboxylase activity with the goal to increase crop yields.