Polarized protein transport and lumen formation during epithelial tissue morphogenesis.

One of the major challenges in biology is to explain how complex tissues and organs arise from the collective action of individual polarized cells. The best-studied model of this process is the cross talk between individual epithelial cells during their polarization to form the multicellular epithelial lumen during tissue morphogenesis. Multiple mechanisms of apical lumen formation have been proposed. Some epithelial lumens form from preexisting polarized epithelial structures. However, de novo lumen formation from nonpolarized cells has recently emerged as an important driver of epithelial tissue morphogenesis, especially during the formation of small epithelial tubule networks. In this review, we discuss the latest findings regarding the mechanisms and regulation of de novo lumen formation in vitro and in vivo.

LC Domain-Mediated Coalescence Is Essential for Otu Enzymatic Activity to Extend Drosophila Lifespan.

In eukaryotic cells, RNA-binding proteins (RBPs) interact with RNAs to form ribonucleoprotein complexes (RNA granules) that have long been thought to regulate RNA fate or activity. Emerging evidence suggests that some RBPs not only bind RNA but also possess enzymatic activity related to ubiquitin regulation, raising important questions of whether these RBP-formed RNA granules regulate ubiquitin signaling and related biological functions. Here, we show that Drosophila Otu binds RNAs and coalesces to membrane-less biomolecular condensates via its intrinsically disordered low-complexity domain, and coalescence represents a functional state for Otu exerting deubiquitinase activity. Notably, coalescence-mediated enzymatic activity of Otu is positively regulated by its bound RNAs and co-partner Bam. Further genetic analysis reveals that the Otu/Bam deubiquitinase complex and dTraf6 constitute a feedback loop to maintain intestinal immune homeostasis during aging, thereby controlling longevity. Thus, regulated biomolecular condensates may represent a mechanism that controls dynamic enzymatic activities and related biological processes.

A global test of hybrid ancestry from genome-scale data.

Methods based on the multi-species coalescent have been widely used in phylogenetic tree estimation using genome-scale DNA sequence data to understand the underlying evolutionary relationship between the sampled species. Evolutionary processes such as hybridization, which creates new species through interbreeding between two different species, necessitate inferring a species network instead of a species tree. A species tree is strictly bifurcating and thus fails to incorporate hybridization events which require an internal node of degree three. Hence, it is crucial to decide whether a tree or network analysis should be performed given a DNA sequence data set, a decision that is based on the presence of hybrid species in the sampled species. Although many methods have been proposed for hybridization detection, it is rare to find a technique that does so globally while considering a data generation mechanism that allows both hybridization and incomplete lineage sorting. In this paper, we consider hybridization and coalescence in a unified framework and propose a new test that can detect whether there are any hybrid species in a set of species of arbitrary size. Based on this global test of hybridization, one can decide whether a tree or network analysis is appropriate for a given data set.

Top-down and bottom-up cohesiveness in microbial community coalescence.

Microbial communities frequently invade one another as a whole, a phenomenon known as community coalescence. Despite its potential importance for the assembly, dynamics, and stability of microbial consortia, as well as its prospective utility for microbiome engineering, our understanding of the processes that govern it is still very limited. Theory has suggested that microbial communities may exhibit cohesiveness in the face of invasions emerging from collective metabolic interactions across microbes and their environment. This cohesiveness may lead to correlated invasional outcomes, where the fate of a given taxon is determined by that of other members of its community-a hypothesis known as ecological coselection. Here, we have performed over 100 invasion and coalescence experiments with microbial communities of various origins assembled in two different synthetic environments. We show that the dominant members of the primary communities can recruit their rarer partners during coalescence (top-down coselection) and also be recruited by them (bottom-up coselection). With the aid of a consumer-resource model, we found that the emergence of top-down or bottom-up cohesiveness is modulated by the structure of the underlying cross-feeding networks that sustain the coalesced communities. The model also predicts that these two forms of ecological coselection cannot co-occur under our conditions, and we have experimentally confirmed that one can be strong only when the other is weak. Our results provide direct evidence that collective invasions can be expected to produce ecological coselection as a result of cross-feeding interactions at the community level.

Stochastic particle unbinding modulates growth dynamics and size of transcription factor condensates in living cells.

Liquid-liquid phase separation (LLPS) is emerging as a key physical principle for biological organization inside living cells, forming condensates that play important regulatory roles. Inside living nuclei, transcription factor (TF) condensates regulate transcriptional initiation and amplify the transcriptional output of expressed genes. However, the biophysical parameters controlling TF condensation are still poorly understood. Here we applied a battery of single-molecule imaging, theory, and simulations to investigate the physical properties of TF condensates of the progesterone receptor (PR) in living cells. Analysis of individual PR trajectories at different ligand concentrations showed marked signatures of a ligand-tunable LLPS process. Using a machine learning architecture, we found that receptor diffusion within condensates follows fractional Brownian motion resulting from viscoelastic interactions with chromatin. Interestingly, condensate growth dynamics at shorter times is dominated by Brownian motion coalescence (BMC), followed by a growth plateau at longer timescales that result in nanoscale condensate sizes. To rationalize these observations, we extended on the BMC model by including the stochastic unbinding of particles within condensates. Our model reproduced the BMC behavior together with finite condensate sizes at the steady state, fully recapitulating our experimental data. Overall, our results are consistent with condensate growth dynamics being regulated by the escaping probability of PR molecules from condensates. The interplay between condensation assembly and molecular escaping maintains an optimum physical condensate size. Such phenomena must have implications for the biophysical regulation of other nuclear condensates and could also operate in multiple biological scenarios.

A comprehensive phylogenomic study unveils evolutionary patterns and challenges in the mitochondrial genomes of Carcharhiniformes: A focus on Triakidae.

The complex evolutionary patterns in the mitochondrial genome (mitogenome) of the most species-rich shark order, the Carcharhiniformes (ground sharks) has led to challenges in the phylogenomic reconstruction of the families and genera belonging to the order, particularly the family Triakidae (houndsharks). The current state of Triakidae phylogeny remains controversial, with arguments for both monophyly and paraphyly within the family. We hypothesize that this variability is triggered by the selection of different a priori partitioning schemes to account for site and gene heterogeneity within the mitogenome. Here we used an extensive statistical framework to select the a priori partitioning scheme for inference of the mitochondrial phylogenomic relationships within Carcharhiniformes, tested site heterogeneous CAT + GTR + G4 models and incorporated the multi-species coalescent model (MSCM) into our analyses to account for the influence of gene tree discordance on species tree inference. We included five newly assembled houndshark mitogenomes to increase resolution of Triakidae. During the assembly procedure, we uncovered a 714 bp-duplication in the mitogenome of Galeorhinus galeus. Phylogenetic reconstruction confirmed monophyly within Triakidae and the existence of two distinct clades of the expanded Mustelus genus. The latter alludes to potential evolutionary reversal of reproductive mode from placental to aplacental, suggesting that reproductive mode has played a role in the trajectory of adaptive divergence. These new sequences have the potential to contribute to population genomic investigations, species phylogeography delineation, environmental DNA metabarcoding databases and, ultimately, improved conservation strategies for these ecologically and economically important species.

Direct Nanosecond Multiframe Imaging of Irreversible Dynamics in 4D Electron Microscopy.

Irreversible ultrafast events are prevalent in nature, yet their capture in real time poses significant challenges. Traditional single-shot imaging technologies, which utilize a single optical pump and single delayed electron probe, offer high spatiotemporal resolution but fail to capture the entire dynamic evolutions. Here, we introduce a novel imaging method employing a single optical pump and delayed multiple electron probes. This approach, facilitated by an innovative deflector in ultrafast electron microscopy, enables the acquisition of nine frames per exposure, paving the way for statistical and quantitative analyses. We have developed an algorithm that corrects frame-by-frame distortions, realizing a cross-correlation enhancement of ∼26%. Achieving ∼12 nm and 20 ns resolution, our method allows for the comprehensive visualization of laser-induced behaviors in Au nanoparticles, including merging, jumping, and collision processes. Our results demonstrate the capability of this multiframe imaging technique to document irreversible processes across materials science and biology with unprecedented nanometer-nanosecond precision.

In Situ TEM Tracking of Disconnection Motion and Atomic Cooperative Reorientation in the Oriented Attachment of Pt Nanoparticles.

The oriented attachment (OA) of nanoparticles (NPs) is an important crystal growth mechanism in many materials. However, a comprehensive understanding of the atomic-scale alignment and attachment processes is still lacking. We conducted in situ atomic resolution studies using high-resolution transmission electron microscopy to reveal how two Pt NPs coalesce into a single particle via OA, which involves the formation of atomic-scale links and a grain boundary (GB) between the NPs, as well as GB migration. Density functional theory calculations showed that the system energy changes as a function of the number of disconnections during the coalescence process. Additionally, the formation and annihilation processes of disconnection are always accompanied by the cooperative reorientation motion of atoms. These results further elucidate the growth mechanism of OA at the atomic scale, providing microscopic insights into OA dynamics and a framework for the development of processing strategies for nanocrystalline materials.

Inference of Coalescence Times and Variant Ages Using Convolutional Neural Networks.

Accurate inference of the time to the most recent common ancestor (TMRCA) between pairs of individuals and of the age of genomic variants is key in several population genetic analyses. We developed a likelihood-free approach, called CoalNN, which uses a convolutional neural network to predict pairwise TMRCAs and allele ages from sequencing or SNP array data. CoalNN is trained through simulation and can be adapted to varying parameters, such as demographic history, using transfer learning. Across several simulated scenarios, CoalNN matched or outperformed the accuracy of model-based approaches for pairwise TMRCA and allele age prediction. We applied CoalNN to settings for which model-based approaches are under-developed and performed analyses to gain insights into the set of features it uses to perform TMRCA prediction. We next used CoalNN to analyze 2,504 samples from 26 populations in the 1,000 Genome Project data set, inferring the age of ∼80 million variants. We observed substantial variation across populations and for variants predicted to be pathogenic, reflecting heterogeneous demographic histories and the action of negative selection. We used CoalNN's predicted allele ages to construct genome-wide annotations capturing the signature of past negative selection. We performed LD-score regression analysis of heritability using summary association statistics from 63 independent complex traits and diseases (average N=314k), observing increased annotation-specific effects on heritability compared to a previous allele age annotation. These results highlight the effectiveness of using likelihood-free, simulation-trained models to infer properties of gene genealogies in large genomic data sets.

The isotope distribution: A rose with thorns.

The isotope distribution, which reflects the number and probabilities of occurrence of different isotopologues of a molecule, can be theoretically calculated. With the current generation of (ultra)-high-resolution mass spectrometers, the isotope distribution of molecules can be measured with high sensitivity, resolution, and mass accuracy. However, the observed isotope distribution can differ substantially from the expected isotope distribution. Although differences between the observed and expected isotope distribution can complicate the analysis and interpretation of mass spectral data, they can be helpful in a number of specific applications. These applications include, yet are not limited to, the identification of peptides in proteomics, elucidation of the elemental composition of small organic molecules and metabolites, as well as wading through peaks in mass spectra of complex bioorganic mixtures such as petroleum and humus. In this review, we give a nonexhaustive overview of factors that have an impact on the observed isotope distribution, such as elemental isotope deviations, ion sampling, ion interactions, electronic noise and dephasing, centroiding, and apodization. These factors occur at different stages of obtaining the isotope distribution: during the collection of the sample, during the ionization and intake of a molecule in a mass spectrometer, during the mass separation and detection of ionized molecules, and during signal processing.

The genomic diversity of the Eliurus genus in northern Madagascar with a putative new species.

Madagascar exhibits extraordinarily high level of species richness and endemism, while being severely threatened by habitat loss and fragmentation (HL&F). In front of these threats to biodiversity, conservation effort can be directed, for instance, in the documentation of species that are still unknown to science, or in investigating how species respond to HL&F. The tufted-tail rats genus (Eliurus spp.) is the most speciose genus of endemic rodents in Madagascar, with 13 described species, which occupy two major habitat types: dry or humid forests. The large species diversity and association to specific habitat types make the Eliurus genus a suitable model for investigating species adaptation to new environments, as well as response to HL&F (dry vs humid). In the present study, we investigated Eliurus spp. genomic diversity across northern Madagascar, a region covered by both dry and humid fragmented forests. From the mitochondrial DNA (mtDNA) and nuclear genomic (RAD-seq) data of 124 Eliurus individuals sampled in poorly studied forests of northern Madagascar, we identified an undescribed Eliurus taxon (Eliurus sp. nova). We tested the hypothesis of a new Eliurus species using several approaches: i) DNA barcoding; ii) phylogenetic inferences; iii) species delimitation tests based on the Multi-Species Coalescent (MSC) model, iv) genealogical divergence index (gdi); v) an ad-hoc test of isolation-by-distance within versus between sister-taxa, vi) comparisons of %GC content patterns and vii) morphological analyses. All analyses support the recognition of the undescribed lineage as a putative distinct species. In addition, we show that Eliurus myoxinus, a species known from the dry forests of western Madagascar, is, surprisingly, found mostly in humid forests in northern Madagascar. In conclusion, we discuss the implications of such findings in the context of Eliurus species evolution and diversification, and use the distribution of northern Eliurus species as a proxy for reconstructing past changes in forest cover and vegetation type in northern Madagascar.

Coarsening of Quasi Two-Dimensional Emulsions Formed by Islands in Free-Standing Smectic Films.

We study the coarsening behavior of assemblies of islands on smectic A freely suspended films in ISS microgravity experiments. The islands can be regarded as liquid inclusions in a two-dimensional fluid in analogy to liquid droplets of the discontinuous phase of an emulsion. The coarsening is effectuated by two processes, predominantly by island coalescence, but to some extend also by Ostwald ripening, whereby large islands grow at the expense of surrounding smaller ones. A peculiarity of this system is that the continuous and the discontinuous phases consist of the same material. We determine the dynamics, analyze the self-similar aging of the island size distribution and discuss characteristic exponents of the mean island growth.

Divergence and reticulation in the Mexican white oaks: ecological and phylogenomic evidence on species limits and phylogenetic networks in the Quercus laeta complex (Fagaceae).

BACKGROUND AND AIMS: Introgressive hybridization poses a challenge to taxonomic and phylogenetic understanding of taxa, particularly when there are high numbers of co-occurring, intercrossable species. The genus Quercus exemplifies this situation. Oaks are highly diverse in sympatry and cross freely, creating syngameons of interfertile species. Although a well-resolved, dated phylogeny is available for the American oak clade, evolutionary relationships within many of the more recently derived clades remain to be defined, particularly for the young and exceptionally diverse Mexican white oak clade. Here, we adopted an approach bridging micro- and macroevolutionary scales to resolve evolutionary relationships in a rapidly diversifying clade endemic to Mexico. METHODS: Ecological data and sequences of 155 low-copy nuclear genes were used to identify distinct lineages within the Quercus laeta complex. Concatenated and coalescent approaches were used to assess the phylogenetic placement of these lineages relative to the Mexican white oak clade. Phylogenetic network methods were applied to evaluate the timing and genomic significance of recent or historical introgression among lineages. KEY RESULTS: The Q. laeta complex comprises six well-supported lineages, each restricted geographically and with mostly divergent climatic niches. Species trees corroborated that the different lineages are more closely related to other species of Mexican white oaks than to each other, suggesting that this complex is polyphyletic. Phylogenetic networks estimated events of ancient introgression that involved the ancestors of three present-day Q. laeta lineages. CONCLUSIONS: The Q. laeta complex is a morphologically and ecologically related group of species rather than a clade. Currently, oak phylogenetics is at a turning point, at which it is necessary to integrate phylogenetics and ecology in broad regional samples to figure out species boundaries. Our study illuminates one of the more complicated of the Mexican white oak groups and lays groundwork for further taxonomic study.

Modelling of mixed-mechanism stimulation for the enhancement of geothermal reservoirs.

Hydraulic stimulation is a critical process for increasing the permeability of fractured geothermal reservoirs. This technique relies on coupled hydromechanical processes induced through pressurized fluid injection into the rock formation. The injection of fluids causes poromechanical stress changes that can lead to fracture slip and shear dilation, as well as tensile fracture opening and propagation, so-called mixed-mechanism stimulation. The effective permeability of the rock is particularly enhanced when new fractures connect with pre-existing fractures. While hydraulic stimulation can significantly improve the productivity of fractured geothermal reservoirs, the process is also related to induced seismicity. Hence, understanding the coupled physics is central, for both reservoir engineering and seismic risk mitigation. This article presents a modelling approach for simulating the deformation, propagation and coalescence of fractures in porous media under the influence of anisotropic stress and fluid injection. It uses a coupled hydromechanical model for poroelastic, fractured media. Fractures are governed by contact mechanics and a fracture propagation model. For numerical solutions, we employ a two-level approach, combining a finite volume method for poroelasticity with a finite element method for fracture propagation. The study investigates the impact of injection rate, matrix permeability and stress anisotropy on stimulation outcomes.This article is part of the theme issue 'Induced seismicity in coupled subsurface systems'.

Community coalescence under variable hydrochemical conditions of the Chesapeake Bay shaped bacterial diversity and functional traits.

Community coalescence related to bacterial mixing events regulates community characteristics and affects the health of estuary ecosystems. At present, bacterial coalescence and its driving factors are still unclear. The present study used a dataset from the Chesapeake Bay (2017) to address how bacterial community coalescence in response to variable hydrochemistry in estuarine ecosystems. We determined that variable hydrochemistry promoted the deterioration of water quality. Temperature, orthophosphate, dissolved oxygen, chlorophyll a, Secchi disk depth, and dissolved organic phosphorus were the key environmental factors driving community coalescence. Bacteria with high tolerance to environmental change were the primary taxa accumulated in community coalescence, and the significance of deterministic processes to communities was revealed. Community coalescence was significantly correlated with the pathways of metabolism and organismal systems, and promoted the co-occurrence of antibiotic resistance and virulence factor genes. Briefly, community coalescence under variable hydrochemical conditions shaped bacterial diversity and functional traits, to optimise strategies for energy acquisition and lay the foundation for alleviating environmental pressures. However, potential pathogenic bacteria in community coalescence may be harmful to human health and environmental safety. The present study provides a scientific reference for ecological management of estuaries.

In Situ Transmission Electron Microscopy Investigation on Oriented Attachment of Nanodiamonds.

Oriented attachment (OA) plays an important role in the assembly of nanoparticles and the regulation of their size and morphology, which is expected to be an effective means to modulate the properties of nanodiamonds (NDs). However, there remains a dearth of comprehensive investigation into the OA mechanism of NDs. Using in situ transmission electron microscopy, we conducted atomic-resolution investigation on the OA events of ND pairs under electron beam irradiation. The occurrence of an OA event is contingent upon the alignment between two ND surfaces, and the coalesced particles undergo recrystallization to form spherical shapes. Both experimental observations and molecular dynamics (MD) simulations reveal that ND pairs exhibit a preference for coalescing along the {111} surfaces. Additionally, MD simulations indicate that kinetic factors, such as contact surface area and contact angle, also influence the coalescence process.

Assessment of spilled oil dispersion affected by dispersant: Characteristic, stability, and related mechanism.

Oil dispersion, a crucial process in oil transport, involves the detachment of oil droplets from slicks and their introduction into the water column, influencing subsequent oil migration and transformation. This study examines oil dispersion, considering characteristics, stability, and mechanisms, while evaluating the impact of dispersants and salinity. Results show the significant role of surfactant type in dispersants on oil dispersion characteristics, with anionic surfactants exhibiting higher sensitivity to salinity changes compared to nonionic surfactants. The dispersion efficiency varies with salinity, with anionic surfactants performing better in low salinity (<20‰) and nonionic surfactants showing superior performance at 30-35‰ salinities. Rheological analysis illustrates the breakup and coalescence of oil droplets within the shear rates of breaking waves. An increase in interfacial film rigidity impedes the coalescence of oil droplets, contributing to the dynamic stability of the oil-water hybrid system. The use of GM-2, a nonionic dispersant, results in the formation of a solid-like interface, characterized by increased elastic modulus, notably at 20‰ salinity. However, stable droplet size distribution (DSD) at 35‰ salinity for 60 h suggests droplets can remain dispersed in seawater. The enhancement of stability of oil dispersion is interpreted as the result of two mechanisms: stabilizing DSD and developing the strength of viscoelastic interfacial film. These findings offer insights into oil dispersion dynamics, highlighting the importance of surfactant selection and salinity in governing dispersion behavior, and elucidating mechanisms underlying dispersion stability.

A novel physical-biochemical treatment of refinery wastewater.

As of 2022, China has achieved a crude oil processing capacity of 918 million tons, leading to a notable escalation in the production of refinery wastewater. The composition of refinery wastewater is intricate and diverse, posing a substantial challenge to its treatment. In order to facilitate appropriate discharge or reuse, an exhaustive separation process is imperative for refinery wastewater. Conventional pre-treatment processes typically employ inclined plate separators and dissolved air flotation (DAF) for the removal of oil and suspended solids (SS), while sequencing batch reactor (SBR), oxidation ditch, or biological aerated filter (BAF) are employed for the biological treatment process. However, these approaches encounter challenges such as a large spatial footprint, suboptimal treatment efficiency, and high energy consumption. In response to these challenges, this study introduces a novel integrated apparatus consisting of a high-efficiency oil remover (HEOR), coalescence oil remover (COR), and an airlift-enhanced loop bioreactor (AELR). A pilot-scale test was conducted to evaluate the performance of this integrated system in practical field applications. The pilot-scale tests reveal that, without the addition of chemical agents, the petroleum removal efficiency of "HEOR + COR" system was 1.2 times that of DAF. Compared with the SBR system, AELR's volume loading was increased by 1.56 times. The effluent quality achieved in the pilot-scale tests attained parity with that the original process. The "HEOR + COR + AELR" system exhibited energy and carbon emissions reduction of 28% and 30% compared to the "DAF + SBR" system, respectively. Therefore, the operating costs was reduced by approximate 1 Chinese Yuan (CNY) per ton of treated water. This technological advancement serves as a valuable reference for the implementation of low-carbon treatment of refinery wastewater.

Capillarity in Interfacial Liquids and Marbles: Mechanisms, Properties, and Applications.

The mechanics of capillary force in biological systems have critical roles in the formation of the intra- and inter-cellular structures, which may mediate the organization, morphogenesis, and homeostasis of biomolecular condensates. Current techniques may not allow direct and precise measurements of the capillary forces at the intra- and inter-cellular scales. By preserving liquid droplets at the liquid-liquid interface, we have discovered and studied ideal models, i.e., interfacial liquids and marbles, for understanding general capillary mechanics that existed in liquid-in-liquid systems, e.g., biomolecular condensates. The unexpectedly long coalescence time of the interfacial liquids revealed that the Stokes equation does not hold as the radius of the liquid bridge approaches zero, evidencing the existence of a third inertially limited viscous regime. Moreover, liquid transport from a liquid droplet to a liquid reservoir can be prohibited by coating the droplet surface with hydrophobic or amphiphilic particles, forming interfacial liquid marbles. Unique characteristics, including high stability, transparency, gas permeability, and self-assembly, are observed for the interfacial liquid marbles. Phase transition and separation induced by the formation of nanostructured materials can be directly observed within the interfacial liquid marbles without the need for surfactants and agitation, making them useful tools to research the interfacial mechanics.

Effect of pH on the emulsifying performance of protein-polysaccharide complexes.

BACKGROUND: Protein-polysaccharide complexes have been successfully used for emulsion stabilization. However, it is unclear how the complex's surface charge influences aggregation stability and coalescence stability of emulsions, and whether a low charged interfacial film can still maintain the coalescence stability of oil droplets. In the present study, the effects of pH (around the pI of protein) on the aggregation and coalescence stability of emulsions were investigated. RESULTS: Whey protein isolate (WPI) and peach gum polysaccharides (PGP) complexes (WPI-PGP complexes) were synthesized at pH 3, 4 and 5. Their sizes were 598, 274 and 183 nm, respectively, and their ζ-potentials were +2.9, -8.6 and -22.8 mV, respectively. Interface rheological experiments showed that WPI-PGP complex at pH 3 had the lowest interfacial tension, and formed the softest film compared to the complexes at pH 4 and 5. Microfluidic experiments showed that all WPI-PGP complexes were able to stabilize droplets against coalescence within short timescales (milliseconds). At pH 3, no coalescence was observed even under conditions where the continuous phase flow influenced the shape of oil droplets (from spheres to ellipsoids). At pH 4 and 5, the model emulsions were stable over 16 days of storage, extensive aggregation and creaming occurred at pH 3 after 8 days. Importantly, no coalescence took place. CONCLUSION: The present study confirmed that the aggregation stability of the emulsions was mainly determined by the surface charge of the complex, whereas the coalescence stability of emulsions is expectedly determined by steric repulsion, providing new insights into how to prepare stable food emulsions. © 2024 Society of Chemical Industry.