Critical Assessment of Condensate Boundaries in Dual-Color Single Particle Tracking.

Biomolecular condensates are membraneless cellular compartments generated by phase separation that regulate a broad variety of cellular functions by enriching some biomolecules while excluding others. Live-cell single particle tracking of individual fluorophore-labeled condensate components has provided insights into a condensate's mesoscopic organization and biological functions, such as revealing the recruitment, translation, and decay of RNAs within ribonucleoprotein (RNP) granules. Specifically, during dual-color tracking, one imaging channel provides a time series of individual biomolecule locations, while the other channel monitors the location of the condensate relative to these molecules. Therefore, an accurate assessment of a condensate's boundary is critical for combined live-cell single particle-condensate tracking. Despite its importance, a quantitative benchmarking and objective comparison of the various available boundary detection methods is missing due to the lack of an absolute ground truth for condensate images. Here, we use synthetic data of defined ground truth to generate noise-overlaid images of condensates with realistic phase separation parameters to benchmark the most commonly used methods for condensate boundary detection, including an emerging machine-learning method. We find that it is critical to carefully choose an optimal boundary detection method for a given dataset to obtain accurate measurements of single particle-condensate interactions. The criteria proposed in this study to guide the selection of an optimal boundary detection method can be broadly applied to imaging-based studies of condensates.

Biomolecular condensates in kidney physiology and disease.

The regulation and preservation of distinct intracellular and extracellular solute microenvironments is crucial for the maintenance of cellular homeostasis. In mammals, the kidneys control bodily salt and water homeostasis. Specifically, the urine-concentrating mechanism within the renal medulla causes fluctuations in extracellular osmolarity, which enables cells of the kidney to either conserve or eliminate water and electrolytes, depending on the balance between intake and loss. However, relatively little is known about the subcellular and molecular changes caused by such osmotic stresses. Advances have shown that many cells, including those of the kidney, rapidly (within seconds) and reversibly (within minutes) assemble membraneless, nano-to-microscale subcellular assemblies termed biomolecular condensates via the biophysical process of hyperosmotic phase separation (HOPS). Mechanistically, osmotic cell compression mediates changes in intracellular hydration, concentration and molecular crowding, rendering HOPS one of many related phase-separation phenomena. Osmotic stress causes numerous homo-multimeric proteins to condense, thereby affecting gene expression and cell survival. HOPS rapidly regulates specific cellular biochemical processes before appropriate protective or corrective action by broader stress response mechanisms can be initiated. Here, we broadly survey emerging evidence for, and the impact of, biomolecular condensates in nephrology, where initial concentration buffering by HOPS and its subsequent cellular escalation mechanisms are expected to have important implications for kidney physiology and disease.

Cross-linking and self-assembly synthesis of tannin-based carbon frameworks cathode for Zn-ion hybrid supercapacitors.

Carbon frameworks with well-developed porosity present broad application prospects in energy-related materials, and green preparation still face challenges. Herein, the tannins-derived framework-like carbon material is obtained by cross-linking and self-assembly strategy.The phenolic hydroxyl and quinones in tannin cross-linking react with the amine groups in the methenamine by simple stirring, which drives the self-assembly of tannins and methenamine,contributing to the reaction products being precipitated in solution as aggregates with framework-like structure. The porosity and micromorphology of framework-like structures are further enriched by the thermal stability difference between tannin and methenamine. The methenamine of framework-like structures is entirely removed by the sublimation and decomposition and the tannin is transformed into carbon materials inheriting framework-like structures after the carbonization, which offers the path for rapid electron transport. The framework-like structure, excellent specific surface area and nitrogen doping give the assembled Zn-ion hybrid supercapacitors a superior specific capacitance of 165.3 mAh·g-1 (350.4 F·g-1). This device could be charged to 1.87 V to power the bulb by using solar panels. This study proves that the tannin-derived framework-like carbon is a promising electrode of the Zn-ion hybrid supercapacitors, which is beneficial for value-added and industrial supercapacitors application of green feedstocks.

Inhibition of FAM46/TENT5 activity by BCCIPα adopting a unique fold.

The FAM46 (also known as TENT5) proteins are noncanonical poly(A) polymerases (PAPs) implicated in regulating RNA stability. The regulatory mechanisms of FAM46 are poorly understood. Here, we report that the nuclear protein BCCIPα, but not the alternatively spliced isoform BCCIPß, binds FAM46 and inhibits their PAP activity. Unexpectedly, our structures of the FAM46A/BCCIPα and FAM46C/BCCIPα complexes show that, despite sharing most of the sequence and differing only at the C-terminal portion, BCCIPα adopts a unique structure completely different from BCCIPß. The distinct C-terminal segment of BCCIPα supports the adoption of the unique fold but does not directly interact with FAM46. The ß sheets in BCCIPα and FAM46 pack side by side to form an extended ß sheet. A helix-loop-helix segment in BCCIPα inserts into the active site cleft of FAM46, thereby inhibiting the PAP activity. Our results together show that the unique fold of BCCIPα underlies its interaction with and functional regulation of FAM46.

Alloying nickel and cobalt with iron on ZSM-5 for tuning competitive hydrogenation reactions for selective one-pot conversion of furfural to gamma-valerolactone.

One-pot conversion of furfural, a biomass-derived platform chemical, to gamma-valerolactone (GVL), a fuel additive and green solvent, involves multiple steps of hydrogenation. Among these reactions, the deep hydrogenation of the furan ring in furfural interrupts GVL formation over Ni or Co-based catalysts. In this study, a method of alloying Ni and Co with Fe over a ZSM-5 support was proposed for tackling excessive activity of the catalyst for hydrogenation. The results indicated that the formation of binary NiFe and CoFe alloys in Ni-Co-Fe/ZSM-5 enhanced the dispersion of metallic species, reduction of metal oxides, formation of more Lewis acidic sites, and the adsorption of the C-O functionality of the furan ring, while lowering the capability for adsorption/activation of H2 and the adsorption of the CC group of the furan ring. These factors together reduced the activity for the hydrogenation of the furan ring in furfural, but enhanced the hydrogenation of the CO in ethyl levulinate (EL). The kinetic study confirmed that the hydrogenation of EL was the rate-determining step. The coordination of the dual alloys, NiFe and CoFe, in the bifunctional Ni-Co-Fe/ZSM-5 catalyst rendered superior activity for selective one-pot conversion of furfural to GVL with a yield of 85.7%.

Side-by-side versus stent-in-stent bilateral stenting for malignant hilar biliary obstruction: a meta-analysis.

Introduction: Both side-by-side (SBS) and stent-in-stent (SIS) bilateral stenting have been used for patients with malignant hilar biliary obstruction (MHBO). However, it is unclear which technique is better. Aim: This meta-analysis is conducted to investigate the clinical efficacy and safety of SBS and SIS bilateral stenting for patients with MHBO. Material and methods: Relevant studies were searched in PubMed, Embase, Cochrane Library, Wanfang, VIP, and CINK databases. The timeline for the searches was from the establishment of the database to September 2021. The relative outcomes are pooled. Results: A total of 7 studies fulfilled the inclusion criteria and entered into this meta-analysis. The pooled technical success rate was significant higher in the SIS group than that in the SBS group (p = 0.04). The pooled early complication rate was significantly lower in the SIS group than in the SBS group (p = 0.04). The pooled stent re-obstruction rate was significantly lower in the SBS group than in the SIS group (p = 0.04). The pooled stent patency duration was significantly longer in the SBS group than in the SIS group (p = 0.01). The pooled functional success rates (p = 0.79), total complication rates (p = 0.34), and overall survival duration (p = 0.27) were comparable between 2 groups. Egger test did not show any publication bias. Conclusions: When comparing the SBS and SIS bilateral stenting for patients with MHBO, although SIS technique may have the superiorities of technical success and early complication rates, the longer stent patency was achieved by the SBS technique.

Synergy of Oxygen Vacancies and Acid Sites on N-Doped WO3 Nanobelts for Efficient C-C Coupling Synthesis of Benzoin Isopropyl Ether.

The surface property of a photocatalyst, including surface acid sites and oxygen vacancies, plays a pivotal role in photocatalytic organic synthesis reactions. Benzoin isopropyl ether (BIE) is usually produced via polycondensation of benzaldehyde and catalyzed with highly toxic cyanide. Here, we report a green photocatalytic approach for the selective synthesis of BIE over WO3 driven by a green-light-emitting diode. The improved photocatalytic activity can be attributed to the synergy of oxygen vacancies (VOs) and acid sites over N-doped WO3 nanobelts. The results revealed that reactant molecules were predominantly adsorbed and activated on surface oxygen vacancies (VOSs) and the Brønsted acid promoted the etherification reaction; the introduction of VOs and nitrogen altered the band structure and electronic properties, resulting in improved photocatalytic activity. Our work provides an efficient approach to the selective photocatalytic synthesis of organics over photocatalysts with finely tuned surface properties and band structures via defect and doping engineering.

Hydrogen-bonded frameworks crystals-assisted synthesis of flower-like carbon materials with penetrable meso/macropores from heavy fraction of bio-oil for Zn-ion hybrid supercapacitors.

The application of biomass-based carbon materials in electrode materials are usually subject to their deficient adsorption sites as well as sluggish diffusion of electrolyte ions. Herein, flower-like carbons are obtained from the heavy fraction of bio-oil with the auxiliary of Hydrogen-bonded frameworks (HOFs) crystals. During the co-carbonization of the both, the HOFs crystals are removed on account of its poor stability, which directs the formation of flower-like morphology and generates the penetrable meso/macropores across petal-like carbon nanosheets. In addition, the pyrolysis gases serve as the agents for activation to enrich the active sites without the further activation. The degree of graphitization and the contents of pyridine nitrogen for carbon materials could be flexibly adjusted with the contents of HOFs. Owing to the beneficial 3D flower-like structure, high specific surface area (1076 m2/g), large pore volume (2.59 cm3/g), and rational N species, the assembled Zn//BH-4 hybrid supercapacitor reaches a superior energy density of 117.5 Wh/kg at 890 W/kg and maintains 60.7 Wh/kg even at 16.2 kW/kg.

Hyperosmotic phase separation: Condensates beyond inclusions, granules and organelles.

Biological liquid-liquid phase separation has gained considerable attention in recent years as a driving force for the assembly of subcellular compartments termed membraneless organelles. The field has made great strides in elucidating the molecular basis of biomolecular phase separation in various disease, stress response, and developmental contexts. Many important biological consequences of such "condensation" are now emerging from in vivo studies. Here we review recent work from our group and others showing that many proteins undergo rapid, reversible condensation in the cellular response to ubiquitous environmental fluctuations such as osmotic changes. We discuss molecular crowding as an important driver of condensation in these responses and suggest that a significant fraction of the proteome is poised to undergo phase separation under physiological conditions. In addition, we review methods currently emerging to visualize, quantify, and modulate the dynamics of intracellular condensates in live cells. Finally, we propose a metaphor for rapid phase separation based on cloud formation, reasoning that our familiar experiences with the readily reversible condensation of water droplets help understand the principle of phase separation. Overall, we provide an account of how biological phase separation supports the highly intertwined relationship between the composition and dynamic internal organization of cells, thus facilitating extremely rapid reorganization in response to internal and external fluctuations.

Crystal facet-dependent activity of h-WO3 for selective conversion of furfuryl alcohol to ethyl levulinate.

The use of WO3 as an acid catalyst has received extensive attention in recent years. However, the correlation between the catalytic activity and the predominantly exposed surface with varied acidic sites needs further understanding. Herein, the effects of the Brønsted and Lewis acid sites of different crystal facets of WO3 on the catalytic conversion of furfuryl alcohol (FA) to ethyl levulinate (EL) in ethanol were investigated in detail. A yield of EL up to 93.3% over WO3 with the (110) facet exposed was achieved at 170 °C, while FA was mainly converted to polymers over (001) faceted nanosheets and nanobelts with exposed (002) and (100) facets. This was attributed to the different distribution of the acidic sites on different exposed crystal facets. The (110) faceted WO3 possessed abundant and strong Brønsted acid sites, which favored the conversion of FA to EL, while the (100) faceted WO3 with stronger Lewis acid sites and weaker Brønsted acid sites mainly led to the formation of polymers. In addition, the (110) faceted WO3 showed excellent sustainability in comparison with the (100) faceted counterpart.

Structural and Functional Analyses of the FAM46C/Plk4 Complex.

FAM46C, a non-canonical poly(A) polymerase, is frequently mutated in multiple myeloma. Loss of function of FAM46C promotes cell survival of multiple myeloma, suggesting a tumor-suppressive role. FAM46C is also essential for fastening sperm head and flagellum, indispensable for male fertility. The molecular mechanisms of these functions of FAM46C remain elusive. We report the crystal structure of FAM46C to provide the basis for its poly(A) polymerase activity and rationalize mutations associated with multiple myeloma. In addition, we found that FAM46C interacts directly with the serine/threonine kinase Plk4, the master regulator of centrosome duplication. We present the structure of FAM46C in complex with the Cryptic Polo-Box 1-2 domains of Plk4. Our structure-based mutational analyses show that the interaction with Plk4 recruits FAM46C to centrosomes. Our data suggest that Plk4-mediated localization of FAM46C enables its regulation of centrosome structure and functions, which may underlie the roles for FAM46C in cell proliferation and sperm development.

Following the messenger: Recent innovations in live cell single molecule fluorescence imaging.

Messenger RNAs (mRNAs) convey genetic information from the DNA genome to proteins and thus lie at the heart of gene expression and regulation of all cellular activities. Live cell single molecule tracking tools enable the investigation of mRNA trafficking, translation and degradation within the complex environment of the cell and in real time. Over the last 5 years, nearly all tools within the mRNA tracking toolbox have been improved to achieve high-quality multi-color tracking in live cells. For example, the bacteriophage-derived MS2-MCP system has been improved to facilitate cloning and achieve better signal-to-noise ratio, while the newer PP7-PCP system now allows for orthogonal tracking of a second mRNA or mRNA region. The coming of age of epitope-tagging technologies, such as the SunTag, MoonTag and Frankenbody, enables monitoring the translation of single mRNA molecules. Furthermore, the portfolio of fluorogenic RNA aptamers has been expanded to improve cellular stability and achieve a higher fluorescence "turn-on" signal upon fluorogen binding. Finally, microinjection-based tools have been shown to be able to track multiple RNAs with only small fluorescent appendages and to track mRNAs together with their interacting partners. We systematically review and compare the advantages, disadvantages and demonstrated applications in discovering new RNA biology of this refined, expanding toolbox. Finally, we discuss developments expected in the near future based on the limitations of the current methods. This article is categorized under: RNA Export and Localization > RNA Localization RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.

Distribution of the crustal magnetic field in Sichuan-Yunnan region, southwest China.

Based on the new and higher degree geomagnetic model NGDC-720-V3, we have investigated the spatial distribution, the altitude decay characteristics of the crustal magnetic anomaly, the contributions from different wavelength bands to the anomaly, and the relationship among the anomaly, the geological structure, and the geophysical field in Sichuan-Yunnan region of China. It is noted that the most outstanding feature in this area is the strong positive magnetic anomaly in Sichuan Basin, a geologically stable block. Contrasting with this feature, a strong negative anomaly can be seen nearby in Longmen Mountain block, an active block. This contradiction implies a possible relationship between the magnetic field and the geological activity. Completely different feature in magnetic field distribution is seen in the central Yunnan block, another active region, where positive and negative anomalies distribute alternatively, showing a complex magnetic anomaly map. Some fault belts, such as the Longmen Mountain fault, Lijiang-Xiaojinhe fault, and the Red River fault, are the transitional zones of strong and weak or negative and positive anomalies. The corresponding relationship between the magnetic anomaly and the geophysical fields was confirmed.