Global Compaction Research Articles

Histone variant H2A.Z and linker histone H1 influence chromosome condensation in Saccharomyces cerevisiae.

Chromosome condensation is essential for the fidelity of chromosome segregation during mitosis and meiosis. Condensation is associated both with local changes in nucleosome structure and larger-scale alterations in chromosome topology mediated by the condensin complex. We examined the influence of linker histone H1 and variant histone H2A.Z on chromosome condensation in budding yeast cells. Linker histone H1 has been implicated in local and global compaction of chromatin in multiple eukaryotes, but we observe normal condensation of the rDNA locus in yeast strains lacking H1. However, deletion of the yeast HTZ1 gene, coding for variant histone H2A.Z, causes a significant defect in rDNA condensation. Loss of H2A.Z does not change condensin association with the rDNA locus or significantly affect condensin mRNA levels. Prior studies reported that several phenotypes caused by loss of H2A.Z are suppressed by eliminating Swr1, a key component of the SWR complex that deposits H2A.Z in chromatin. We observe that an htz1Δ swr1Δ strain has near-normal rDNA condensation. Unexpectedly, we find that elimination of the linker histone H1 can also suppress the rDNA condensation defect of htz1Δ strains. Our experiments demonstrate that histone H2A.Z promotes chromosome condensation, in part by counteracting activities of histone H1 and the SWR complex.

Single-nucleoid architecture reveals heterogeneous packaging of mitochondrial DNA.

Cellular metabolism relies on the regulation and maintenance of mitochondrial DNA (mtDNA). Hundreds to thousands of copies of mtDNA exist in each cell, yet because mitochondria lack histones or other machinery important for nuclear genome compaction, it remains unresolved how mtDNA is packaged into individual nucleoids. In this study, we used long-read single-molecule accessibility mapping to measure the compaction of individual full-length mtDNA molecules at near single-nucleotide resolution. We found that, unlike the nuclear genome, human mtDNA largely undergoes all-or-none global compaction, with most nucleoids existing in an inaccessible, inactive state. Highly accessible mitochondrial nucleoids are co-occupied by transcription and replication components and selectively form a triple-stranded displacement loop structure. In addition, we showed that the primary nucleoid-associated protein TFAM directly modulates the fraction of inaccessible nucleoids both in vivo and in vitro, acting consistently with a nucleation-and-spreading mechanism to coat and compact mitochondrial nucleoids. Together, these findings reveal the primary architecture of mtDNA packaging and regulation in human cells.

Regional mudstone compaction trends in the Vienna Basin: top seal assessment and implications for uplift history

Seal quality assessment is not only essential in petroleum systems studies but also in the context of other geo energy applications such as underground hydrogen storage. Capillary breakthrough pressure controls top seal capacity in the absence of faults or other discontinuities. In basins that lack measured capillary pressure data (e.g., from drill cores), regional compaction-porosity trends can be used as a first prediction tool to estimate the capillary properties of mudstones. Mathematical compaction models exist but need to be calibrated for each basin. This study aims to establish a compaction trend based on theoretical models, then compare it with theoretical maximum hydrocarbon column heights inferred from true measured capillary pressure curves. Middle to upper Miocene mudstone core samples from the Vienna Basin, covering a broad depth interval from 700 to 3400 m, were investigated by X-ray diffractometry, with an Eltra C/S analyzer, and by Rock–Eval pyrolysis for bulk mineralogy, total organic carbon, and free hydrocarbon contents. Broad ion beam—scanning electron microscopy, mercury intrusion capillary porosimetry, and helium pycnometry were applied to obtain pore structural properties to compare the mathematical compaction models with actual porosity data from the Vienna Basin. Clear decreasing porosity depth trends imply that mechanical compaction was rather uniform in the central Vienna Basin. Comparing the Vienna Basin trend to global mudstone compaction trends, regional uplift causing erosion of up to ~ 500 m upper Miocene strata is inferred. A trend of increasing Rock–Eval parameters S1 and production index [PI = S1/(S1 + S2)] with decreasing capillary sealing capacity of the investigated mudstones possibly indicates vertical hydrocarbon migration through the low-permeable mudstone horizons. This observation must be considered in future top-seal studies for secondary storage applications in the Vienna Basin.

Protein-Inspired Control over Synthetic Polymer Folding for Structured Functional Nanoparticles in Water.

The folding of proteins into functional nanoparticles with defined 3D structures has inspired chemists to create simple synthetic systems mimicking protein properties. The folding of polymers into nanoparticles in water proceeds via different strategies, resulting in the global compaction of the polymer chain. Herein, we review the different methods available to control the conformation of synthetic polymers and collapse/fold them into structured, functional nanoparticles, such as hydrophobic collapse, supramolecular self-assembly, and covalent cross-linking. A comparison is made between the design principles of protein folding to synthetic polymer folding and the formation of structured nanocompartments in water, highlighting similarities and differences in design and function. We also focus on the importance of structure for functional stability and diverse applications in complex media and cellular environments.

Live imaging reveals chromatin compaction transitions and dynamic transcriptional bursting during stem cell differentiation in vivo.

Stem cell differentiation requires dramatic changes in gene expression and global remodeling of chromatin architecture. How and when chromatin remodels relative to the transcriptional, behavioral, and morphological changes during differentiation remain unclear, particularly in an intact tissue context. Here, we develop a quantitative pipeline which leverages fluorescently-tagged histones and longitudinal imaging to track large-scale chromatin compaction changes within individual cells in a live mouse. Applying this pipeline to epidermal stem cells, we reveal that cell-to-cell chromatin compaction heterogeneity within the stem cell compartment emerges independent of cell cycle status, and instead is reflective of differentiation status. Chromatin compaction state gradually transitions over days as differentiating cells exit the stem cell compartment. Moreover, establishing live imaging of Keratin-10 (K10) nascent RNA, which marks the onset of stem cell differentiation, we find that Keratin-10 transcription is highly dynamic and largely precedes the global chromatin compaction changes associated with differentiation. Together, these analyses reveal that stem cell differentiation involves dynamic transcriptional states and gradual chromatin rearrangement.

Revealing the accessibility and surface morphology of the Escherichia coli nucleoid by genetically encoded live-cell single-particle tracking.

Membraneless organelles play a key role in the subcellular organization and regulation of bacterial cells. In particular, the bacterial genome is highly compacted into a membraneless organelle: the nucleoid. The structure and accessibility of the nucleoid significantly influences gene expression, and this morphology varies with growth phase and under various environmental conditions. Therefore, revealing how the DNA meshwork changes as a function of the growth phase will deepen our understanding of how bacteria regulate transcription in response to stress. To realize this goal, we applied single-particle tracking in E. coli and super-resolved the dynamics of an extrinsic 25-nm protein assembly with a well-defined dodecahedron structure: GFP-nanocages (Hsia et al., Nature 2016). By super-resolving the GFP-nanocage positions from log phase to late stationary phase, we observed an increasingly obvious exclusion of the probe by nucleoid, which indicates that the chromosome is compacting and becoming less accessible for gene expression. Our preliminary experiments also found a novel observation: the nucleoid size and compaction are not necessarily correlated. We hypothesize that at the intermediate stage of compaction, cells with small nucleoids may have a relatively low global compaction level because DNA chains are dragged by the force generated by DNA-NAP complex formation, leading to compacted rigid cores surrounded by a loosened DNA meshwork. By measuring the single-molecule step sizes at the periphery of the nucleoid, we understand the rigidity and smoothness of nucleoid surface at various phases. Furthermore, by analyzing the angle distribution within single-particle trajectories, we quantify the orientation of interactions with the nucleoid. The gene expression levels differ with cell growth stage (Verma et al., PLoS Genetics 2019). Our research provides a novel way of understanding how subcellular structure and gene expression are related.

Attention-Guided Pyramid Context Network for Polyp Segmentation in Colonoscopy Images

Recently, deep convolutional neural networks (C-NNs) have provided us an effective tool for automated polyp segmentation in colonoscopy images. However, most CNN-based methods do not fully consider the feature interaction among different layers and often cannot provide satisfactory segmentation performance. In this paper, a novel attention-guided pyramid context network (APCNet) is proposed for accurate and robust polyp segmentation in colonoscopy images. Specifically, considering that different network layers represent the polyp in different aspects, APCNet first extracts multi-layer features in a pyramid structure, then utilizes an attention-guided multi-layer aggregation strategy to refine the context features of each layer by utilizing the complementary information of different layers. To obtain abundant context features, APCNet employs a context extraction module that explores the context information of each layer via local information retainment and global information compaction. Through the top-down deep supervision, our APCNet implements a coarse-to-fine polyp segmentation and finally localizes the polyp region precisely. Extensive experiments on two in-domain and four out-of-domain experiments show that APCNet is comparable to 19 state-of-the-art methods. Moreover, it holds a more appropriate trade-off between effectiveness and computational complexity than these competing methods.

Soil compaction monitoring via photogrammetric settlement measurement – Feasibility study

This paper presents a new method of global compaction monitoring based on surface settlement measurements using the Structure from Motion (SfM) approach. The introduced approach was developed to enhance research on soil compaction. A layer of medium sand was compacted with a plate compactor during the experiment on an outdoor test site. The settlement of the soil surface was measured using close-range photogrammetry and optical level. Furthermore, relationships between settlement and changes in layer density and stiffness were studied. The analysis showed that the Structure from Motion approach allows for monitoring soil surface settlement with excellent resolution and accuracy. Moreover, the change of settlement and dynamic modulus during compaction showed a similar trend. This indicates that the proposed approach is a valuable tool for researchers studying the compaction process. Nevertheless, it implementing such technology in industrial projects still requires further development, especially in improving standardization and automation.

Direct observation of Hsp90-induced compaction in a protein chain.

The chaperone heat shock protein 90 (Hsp90) is well known to undergo important conformational changes, which depend on nucleotide and substrate interactions. Conversely, how the conformations of its unstable and disordered substrates are affected by Hsp90 is difficult to address experimentally yet is central to its function. Here, using optical tweezers, we find that Hsp90 promotes local contractions in unfolded chains that drive their global compaction down to dimensions of folded states. This compaction has a gradual nature while showing small steps, is stimulated by ATP, and performs mechanical work against counteracting forces that expand the chain dimensions. The Hsp90 interactions suppress the formation of larger-scale folded, misfolded, and aggregated structures. The observations support a model in which Hsp90 alters client conformations directly by promoting local intra-chain interactions while suppressing distant ones. We conjecture that chain compaction may be central to how Hsp90 protects unstable clients and cooperates with Hsp70.

Disorder to order transition in cell-ECM systems mediated by cell-cell collective interactions

Cells in functional tissues execute various collective activities to achieve diverse ordered processes including wound healing, organogenesis, and tumor formation. How a group of individually operating cells initiate such complex collective processes is still not clear. Here, we report that cells in 3D extracellular matrix (ECM) initiate collective behavior by forming cell-ECM network when the cells are within a critical distance from each other. We employed compaction of free-floating (FF) 3D collagen gels with embedded fibroblasts as a model system to study collective behavior and found a sharp transition in the amount of compaction as a function of cell-cell distance, reminiscent of phase transition in materials. Within the critical distance, cells remodel the ECM irreversibly, and form dense collagen bridges between each other resulting in the formation of a network. Beyond the critical distance, cells exhibit Brownian dynamics and only deform the matrix reversibly in a transient manner with no memory of history, thus maintaining the disorder. Network formation seems to be a necessary and sufficient condition to trigger collective behavior and a disorder-to order transition. Statement of significanceMacroscopic compaction of in vitro collagen gels is mediated by collective mechanical interaction of cells. Previous studies on cell-induced ECM compaction suggest the existence of a critical cell density and phase transition associated with this phenomenon. Cell-mediated mechanical remodeling and global compaction of ECM has mostly been studied at steady state. Our study reveals a link between a transition in cell dynamics and material microstructure as cells collectively compact collagen gels. It underscores the significance of temporal evolution of these cell-ECM systems in understanding the mechanism of such collective action and provides insights on the process from a mechanistic viewpoint. These insights can be valuable in understanding dynamic pathological processes such as, cancer progression and wound healing, as well as engineering biomaterials and regenerative tissue mimics.

Control and Characterization of the Compactness of Single-Chain Nanoparticles

Polymers when self-cross-linked into single-chain nanoparticles bear some resemblance to folded proteins; yet proteins have clear energy landscapes that determine precisely folded structures, while single-chain polymer nanoparticles (SCNPs) have more undefined structures. There have been initial reports showing that some structural parameters in SCNPs can be controlled, for example, compactness. Here, we construct SCNPs from poly(allylamine) (Mw ∼ 22 000 Da) with dicarboxylic acids (HOOC–R–COOH) in solvent conditions, where initial chains adopt either extended or collapsed conformation. The spacer groups R that we used were −CH2CH2–, −(CH2S)2–, or −(CH2CH2)3–, whose length can be estimated to vary from ∼4 to ∼12 Å. We present a systematic study that uses several characterization techniques (1H NMR diffusion-ordered spectroscopy (DOSY), viscometry, analytical ultracentrifugation, and 1H NMR T2 relaxation) to show that both initial reaction conditions as well as length of cross-linking molecules determine the final compactness of SCNPs. Specifically, when short cross-linking molecules are applied, short-range loops dominate and the cross-linking process fails to achieve global chain compaction, leading to less compact SCNPs. When the chain is precollapsed (0.1 M water solution of NaCl or 10 vol % ethanol as opposed to DI water), the particles resulting after cross-linking are more compact. Of utmost practical relevance, we show that particles that are essentially chemically identical but differ only in compactness have different toxicity when interacting with HeLa cells, the more compact ones being less toxic.

A global chromatin compaction pathway that represses germline gene expression during starvation.

While much is known about how transcription is controlled at individual genes, comparatively little is known about how cells regulate gene expression on a genome-wide level. Here, we identify a molecular pathway in the C. elegans germline that controls transcription globally in response to nutritional stress. We report that when embryos hatch into L1 larvae, they sense the nutritional status of their environment, and if food is unavailable, they repress gene expression via a global chromatin compaction (GCC) pathway. GCC is triggered by the energy-sensing kinase AMPK and is mediated by a novel mechanism that involves the topoisomerase II/condensin II axis acting upstream of heterochromatin assembly. When the GCC pathway is inactivated, then transcription persists during starvation. These results define a new mode of whole-genome control of transcription.

Understanding die compaction of hollow spheres using the multi-particle finite element method (MPFEM)

Powder compaction is a complex manufacturing process, even though the procedural description is simple. While different methods are used in the literature, it is still challenging to understand the governing principles. It is especially challenging for empirical studies to investigate particle-level interactions. Thus, computational analyses are required for particle-level understanding. A wide range of computational methods has been developed, such as the discrete element method (DEM) and the multi-particle finite element method (MPFEM), to characterize powder compaction at the particle level. However, a limited number of studies in the literature have analyzed powder compaction using the 3D multi-particle finite element method. Historically, these studies focus only on solid particles. The compaction behavior of hollow spheres, common to pharmaceutical spray drying, was investigated both computationally and experimentally. In the computational analysis, two different particle sizes with different shell-thicknesses were examined using the 3D multi-particle finite element method. In the experimental study, polymer hydroxypropyl methylcellulose acetate succinate (HPMCAS) particles spray-dried at two different outlet temperatures (45 °C and 80 °C) were used. The results showed that particle diameter/shell-thickness (d/w) plays an essential role in powder compaction behavior. Regardless of the particle size, reducing shell-thickness reduced the required global axial stress to reach equivalent levels of relative density. However, with a constant ratio of d/w, changes to particle size (d) did not significantly influence the global compaction behavior. Similar results were observed in experimental studies. Simulation results showed that thinner-shell particles yield early in the compaction stage. Additionally, both experimentally and computationally, a spherical hollow particle buckling effect was observed. In summary, this study provides new information on how powder compaction behavior was influenced by particle size and particle shell-thickness.

Chromatin accessibility governs the differential response of cancer and Tcells to arginine starvation.

SummaryDepleting the microenvironment of important nutrients such as arginine is a key strategy for immune evasion by cancer cells. Many tumors overexpress arginase, but it is unclear how these cancers, but not T cells, tolerate arginine depletion. In this study, we show that tumor cells synthesize arginine from citrulline by upregulating argininosuccinate synthetase 1 (ASS1). Under arginine starvation, ASS1 transcription is induced by ATF4 and CEBPβ binding to an enhancer within ASS1. T cells cannot induce ASS1, despite the presence of active ATF4 and CEBPβ, as the gene is repressed. Arginine starvation drives global chromatin compaction and repressive histone methylation, which disrupts ATF4/CEBPβ binding and target gene transcription. We find that T cell activation is impaired in arginine-depleted conditions, with significant metabolic perturbation linked to incomplete chromatin remodeling and misregulation of key genes. Our results highlight a T cell behavior mediated by nutritional stress, exploited by cancer cells to enable pathological immune evasion.

DNA sequence-directed cooperation between nucleoid-associated proteins

SummaryNucleoid-associated proteins (NAPs) are a class of highly abundant DNA-binding proteins in bacteria and archaea. While both the composition and relative abundance of the NAPs change during the bacterial growth cycle, surprisingly little is known about their crosstalk in mutually binding and stabilizing higher-order nucleoprotein complexes in the bacterial chromosome. Here, we use atomic force microscopy and solid-state nanopores to investigate long-range nucleoprotein structures formed by the binding of two major NAPs, FIS and H-NS, to DNA molecules with distinct binding site arrangements. We find that spatial organization of the protein binding sites can govern the higher-order architecture of the nucleoprotein complexes. Based on sequence arrangement the complexes differed in their global shape and compaction as well as the extent of FIS and H-NS binding. Our observations highlight the important role the DNA sequence plays in driving structural differentiation within the bacterial chromosome.

Mrc1-Dependent Chromatin Compaction Represses DNA Double-Stranded Break Repair by Homologous Recombination Upon Replication Stress.

The coordination of DNA replication and repair is critical for the maintenance of genome stability. It has been shown that the Mrc1-mediated S phase checkpoint inhibits DNA double-stranded break (DSB) repair through homologous recombination (HR). How the replication checkpoint inhibits HR remains only partially understood. Here we show that replication stress induces the suppression of both Sgs1/Dna2- and Exo1-mediated resection pathways in an Mrc1-dependent manner. As a result, the loading of the single-stranded DNA binding factor replication protein A (RPA) and Rad51 and DSB repair by HR were severely impaired under replication stress. Notably, the deletion of MRC1 partially restored the recruitment of resection enzymes, DSB end resection, and the loading of RPA and Rad51. The role of Mrc1 in inhibiting DSB end resection is independent of Csm3, Tof1, or Ctf4. Mechanistically, we reveal that replication stress induces global chromatin compaction in a manner partially dependent on Mrc1, and this chromatin compaction limits the access of chromatin remodeling factors and HR proteins, leading to the suppression of HR. Our study reveals a critical role of the Mrc1-dependent chromatin structure change in coordinating DNA replication and recombination under replication stress.

Role of Ligand-Binding and Non-Active Site Residues in the Dynamics, Conformational Integrity, and Catalysis of the Disordered Enzyme Monomeric Chorismate Mutase

The dominant view in enzymology is that an increase in structural disorderedness tends to decrease catalytic efficiency. Surprisingly, engineered monomeric chorismate mutase (mCM), an enzyme with properties of molten globule (intrinsically disordered), efficiently catalyses the conversion of chorismate to prephenate. Therefore, here, we investigate the underlying structural plasticity mechanisms that facilitate this catalysis. We generated rationally designed mutations of mCM and used a battery of spectroscopic tests including Forster resonance energy transfer (FRET) and time-resolved fluorescence anisotropy measurements to probe what influences catalysis. We found that the integrity of the secondary structure, and ligand-induced global compaction (disorder-to-order transition) play a crucial role in catalysis. Intriguingly, we find that even minor perturbation in regions distant from the active site can significantly impact the enzyme efficiency by changing the conformation, segmental dynamics, ligand-induced global compaction, and stability.

Intelligent rolling compaction system for earth-rock dams

The compaction quality of earth-rock dams primarily depends on manual control of the compaction parameters during construction and random spot tests after construction. However, manual control of the compaction parameters can result in more control errors and quality defects and cannot satisfy the requirements of construction operations under all weather and extreme conditions. Additionally, spot tests with characteristics such as random and destructive detection, low efficiency, and high costs cannot adequately reflect the compaction status of an entire area or satisfy the requirements of rapid mechanised construction. This paper presents an intelligent rolling compaction method based on a new framework of material-machine-information-machine intelligent decision-making for earth-rock dams. Using the proposed system integration method based on three-layer structure, IRC system can be obtained by integrating the continuous compaction control acoustic wave detection (CAWD) system combined with real-time kinematic global positioning system (RTK-GPS), intelligent decision-making (IDM) system based on the global compaction process-dynamic optimisation method (GCPDOM), unmanned rolling compaction (URC) system based on automatic driving technology, and real-time remote monitoring centre based on the triangle architecture. The implementation of the proposed system in the Qianping Reservoir construction site has shown that its operation is stable and reliable, and it can effectively eliminate the impact of human factors on compaction quality control, thereby significantly improving the compaction quality and construction efficiency of earth-rock dams.

Monitoring global changes in chromatin compaction states upon localized DNA damage with tools of fluorescence anisotropy.

In the eukaryotic nucleus, DNA, packaged in the form of chromatin, is subject to continuous damage. Chromatin has to be remodeled in order to repair such damage efficiently. But compact chromatin may also be more refractory to damage. Chromatin responses during DNA double-strand break (DSB) repair have been studied with biochemistry or as indirect readouts for the physical state of the chromatin at the site of damage. Direct measures of global chromatin compaction upon damage are lacking. We used fluorescence anisotropy imaging of histone H2B-EGFP to interrogate global chromatin compaction changes in response to localized DSBs directly. Anisotropy maps were preserved in fixation and reported on underlying chromatin compaction states. Laser-induced clustered DSBs led to global compaction of even the undamaged chromatin. Live-cell dynamics could be coupled with fixed-cell assays. Repair factors, PARP1 and PCNA, were immediately recruited to the site of damage, though the local enrichment of PCNA persisted longer than that of PARP1. Subsequently, nodes of PCNA that incorporated deoxynucleotide analogs were observed in regions of low-anisotropy open chromatin, even away from the site of damage. Such fluorescence anisotropy–based readout of chromatin compaction may be used in the investigation of different forms of DNA damage.

‐The Influence of Histone Variant H2A.Z and Linker Histone H1 on Saccharomyces cerevisiae Meiosis

Meiosis in Saccharomyces cerevisiae is associated with unique chromosome choreography and chromatin reorganization. In vegetative cells, the histone variant H2A.Z, has a significant role in gene expression, DNA repair, chromosome segregation and maintenance of euchromatin‐heterochromatin boundaries, however, its function in meiosis has not been thoroughly investigated. The linker histone H1 has a role in global gene repression and genome compaction. We have shown that the loss of H1 suppresses some of the defects associated with the absence of H2A.Z. We investigated the impact of histones H2A.Z and H1 on budding yeast meiosis. We found that strains lacking either H2A.Z, H1, or both proteins exhibit wild type levels of sporulation efficiency. H1 does not influence spore viability, whereas the absence of H2A.Z reduces spore viability. Interestingly, the deletion of HHO1 can partially suppress the spore germination defect observed in the absence of H2A.Z. Our results indicate that strains lacking H2A.Z, H1 or both histones have recombination efficiencies similar to those of the wild type. We observe a chromosome axis defect in a subset of cells lacking H2A.Z. Our results suggest that histones H2A.Z and H1 collaborate to influence meiosis in budding yeast.