Clusters Of Sites Research Articles

Rapid profiling of transcription factor-cofactor interaction networks reveals principles of epigenetic regulation.

Transcription factor (TF)-cofactor (COF) interactions define dynamic, cell-specific networks that govern gene expression; however, these networks are understudied due to a lack of methods for high-throughput profiling of DNA-bound TF-COF complexes. Here, we describe the Cofactor Recruitment (CoRec) method for rapid profiling of cell-specific TF-COF complexes. We define a lysine acetyltransferase (KAT)-TF network in resting and stimulated T cells. We find promiscuous recruitment of KATs for many TFs and that 35% of KAT-TF interactions are condition specific. KAT-TF interactions identify NF-κBas a primary regulator of acutely induced histone 3 lysine 27 acetylation (H3K27ac). Finally, we find that heterotypic clustering of CBP/P300-recruiting TFs is a strong predictor of total promoter H3K27ac. Our data support clustering of TF sites that broadly recruit KATs as a mechanism for widespread co-occurring histone acetylation marks. CoRec can be readily applied to different cell systems and provides a powerful approach to define TF-COF networks impacting chromatin state and gene regulation.

Promoting CO2 Electroreduction to Hydrocarbon Products via Sulfur-Enhanced Proton Feeding in Atomically Precise Thiolate-Protected Cu Clusters.

Thiolate-protected Cu clusters with well-defined structures and stable low-coordinated Cu+ species exhibit remarkable potential for the CO2RR and are ideal model catalysts for establishing structure-electrocatalytic property relationships at the atomic level. However, extant Cu clusters employed in the CO2RR predominantly yield 2e- products. Herein, two model Cu4(MMI)4 and Cu8(MMI)4(tBuS)4 clusters (MMI=2-mercapto-1-methylimidazole) are prepared to investigate the synergistic effect of Cu+ and adjacent S sites on the CO2RR. Cu4(MMI)4 can reduce CO2 to deep-reduced products with a 91.0 % Faradaic efficiency (including 53.7 % for CH4) while maintaining remarkable stability. Conversely, Cu8(MMI)4(tBuS)4 shows a remarkable preference for C2+ products, achieving a maximum FE of 58.5 % with a C2+ current density of 152.1 mA⋅cm-2. In situ XAS and ex situ XPS spectra reveal the preservation of Cu+ species in Cu clusters during CO2RR, extensively enhancing the adsorption capacity of *CO intermediate. Moreover, kinetic analysis and theoretical calculations confirm that S sites facilitate H2O dissociation into *H species, which directly participate in the protonation process on adjacent Cu sites for the protonation of *CO to *CHO. This study highlights the important role of Cu-S dual sites in Cu clusters and provides mechanistic insights into the CO2RR pathway at the atomic level.

The role of DNA polymerase I in tolerating single-strand breaks generated at clustered DNA damage in Escherichia coli

Clustered DNA damage, when multiple lesions are generated in close proximity, has various biological consequences, including cell death, chromosome aberrations, and mutations. It is generally perceived as a hallmark of ionizing radiation. The enhanced mutagenic potential of lesions within a cluster has been suggested to result, at least in part, from the selection of the strand with the mutagenic lesion as the preferred template strand, and that this process is relevant to the tolerance of persistent single-strand breaks generated during an attempted repair. Using a plasmid-based assay in Escherichia coli, we examined how the strand bias is affected in mutant strains deficient in different DNA polymerase I activities. Our study revealed that the strand-displacement and 5′-flap endonuclease activities are required for this process, while 3′-to-5′ exonuclease activity is not. We also found the strand template that the mutagenic lesion was located on, whether lagging or leading, had no effect on this strand bias. Our results imply that an unknown pathway operates to repair/tolerate the single-strand break generated at a bi-stranded clustered damage site, and that there exist different backup pathways, depending on which DNA polymerase I activity is compromised.

Развитие ночного туризма: преимущества и недостатки

The article is devoted to the analysis of the features of night tourism, as a recently emerged and not yet widespread type of tourism activity. The work analyzes approaches to the concept of night tourism, its origin, reasons for its growing popularity, foreign practice in implementing night tourism programs using the example of China, Taiwan, Vietnam and other countries. Various forms of nighttime entertainment are generalized, the advantages and disadvantages of night tourism are highlighted, and Russia's capabilities for forming a cluster of nighttime tourist sites are assessed. In conclusion, it is concluded that night tourism effectively complements daytime tourist routes, and has potential for development in Russian cities.

Evolution of liquid phase during homogenous non-equilibrium melting of Ta at superheating temperature.

Homogenous melting at superheating temperature is commonly described by classical nucleation theory (CNT), but the atomic mechanism of the formation and development of critical liquid nuclei is still unclear. Molecular dynamics simulations were conducted to analyze the melting process of Ta. It is found that the process of subcritical liquid clusters evolving into critical liquid nucleus occupies most of the melting time, and merging between neighboring liquid clusters is the main path for subcritical liquid clusters to grow in size. Total melting time is strongly affected by the distribution of formation sites of subcritical liquid clusters, which has been considered random in homogenous melting. This work depicts a clear picture of the formation and development of liquid phase during the homogeneous melting process at superheating temperature and suggests an internal factor of melting mechanism.

Localized Canal Development Model Based on Titled Landscapes on the Grand Canal, Hangzhou Section, China

After the decline of water transportation along the Grand Canal, the integration of urban development and the preservation of cultural heritage along the canal has become imperative. This paper takes the titled landscape as its research perspective and investigates the cultural significance of the canal through its historical, spatial, artistic, and spiritual dimensions, identifying the “Ten Canal Scenes” (TCS) that encapsulate both the canal’s heritage and the unique characteristics of Hangzhou, with the aim of establishing notable urban cultural landmarks. Archival analysis, average nearest neighbor (ANN) analysis, nuclear density analysis, and clustering of resource sites are first used to identify cultural landscape features. Evaluation and decision-making techniques are then used to comprehensively assess and categorize the conservation and utilization value for the TCS based on the value evaluation framework. Finally, it proposes strategies for enhancing the comprehensive values of titled landscapes and addressing socio-economic and cultural dimensions. These efforts seek to reconcile the preservation of the canal’s cultural heritage with the ongoing regeneration and development of the city and propose references for a localized canal development model based on titled landscapes.

Overcoming mechanistic limitations of process-based phenological models: A data clustering method for large-scale applications

Process-based phenological models use thermal requirement (TR) defined by planting date, temperature and photoperiod to predict crop developmental stages. The TR value for a specific developmental stage for a given variety is often presumed to be constant regardless of environmental conditions. We calibrated and compared 12 phenological models using 27-year of observation data of one unique rice (Oryza sativa L.) variety ('Shanyou63') from 46 sites in southern China. Our findings indicated that shifts in environmental conditions significantly affected TR values, e.g., standard deviations of TR at physiological maturation ranged from 83 to 167 °C d. Clustering sites together minimized environmental heterogeneity, and thus minimized the differences in TR for different phenological stages. When the increased from 1 to 24, simulation errors for the 12 models showed a significant decrease across all developmental stages, from 1.8 to 1.4 days for tillering, from 5.3 to 3.7 days for jointing, from 5.6 to 3.9 days for booting, from 4.7 to 3.3 days for heading, and from 6.6 to 3.7 days for physiological maturation. Furthermore, our findings indicate that models featuring a three-segment piecewise linear temperature response function provide a more precise prediction. In contrast, models incorporating a Beta temperature response function have not performed well. This difference is attributed to different mechanisms used to describe the response of crop development rate to temperature, particularly at non-optimum temperatures. The impact of the photoperiod response function on prediction accuracy became significant with the expansion of scale. Our results demonstrate that clustering method effectively compensates for the lack of crop adaptation processes in common phenological models, leading to significantly improved phenological prediction accuracy in regions with environmental diversity.

A study on the association between insulin resistance and genome-wide DNA methylation based on Shanghai monozygotic twins

Objective: To explore the association between insulin resistance (IR) and genome-wide DNA methylation based on Shanghai twin study. Methods: Monozygotic twins (MZ) from Shanghai were recruited during 2012-2013, 2017-2018, and 2022-2023. Data were collected by questionnaire survey, physical examination and laboratory tests. Genome-wide DNA methylation was quantified. Generalized linear mixed effect model was applied to analyze the association between methylation level at each site and homeostatic model assessment 2-insulin resistance (HOMA2-IR). Non-paired and paired designs were used to assess the association between DNA methylation and phenotype of IR. Cluster analysis was conducted to identify the clusters of top significant sites. Generalized linear regression was performed to examine the differential methylation patterns from clusters. Results: A total of 100 MZ pairs were included in this study. Hypermethylated cg10535199-2q23.1 (β=0.74%, P=1.51×10-7, OR=1.06, 95%CI: 1.03-1.09) and ch.17.49619327-SPOP (β=0.23%, P=7.54×10-7, OR=1.17, 95%CI: 1.08-1.28) were identified with suggestive significance. After correcting for multiple testing, no sites reached genome-wide significance. There was no statistical significance in the paired analysis. Two clusters with hypomethylated (β=-0.39%, P<0.001) and hypermethylated (β=0.47%, P<0.001) patterns were observed for HOMA2-IR. Conclusions: IR was significantly associated with DNA methylation, and genetic factors might contribute to the association.

Triiron Complexes Featuring Azadiphosphine Related to the Active Site of [FeFe]-Hydrogenases: Their Redox Behavior and Protonation.

The design of iron clusters featuring a bimetallic core and several protonation sites in the second coordination sphere of the metal centers is important for modeling the activity of polymetallic active sites such as the H-cluster of [FeFe]-hydrogenases. For this purpose, the syntheses of complexes [Fe3(CO)5(κ2-PPh2NR2)(μ-pdt)2] (R = Ph (1), Bn (2)) and [Fe3(CO)5(κ2-PPh2NR2)(μ-adtBn)(μ-pdt)] (R = Ph (3), Bn (4)) were carried out by reacting hexacarbonyl precursors [Fe2(CO)6(µ-xdt)] (xdt = pdt (propanedithiolate), adtBn (azadithiolate) with mononuclear complexes [Fe(κ2-pdt)(CO)2(κ2-PPh2NR2)] (PPh2NR2 = (PPhCH2NRCH2)2, R = Ph, Bn) in order to introduce amine functions, through well-known PPh2NR2 diphosphine, into the vicinity of the triiron core. The investigation of the reactivity of these triiron species towards the proton (in the presence of CF3SO3H) and the influence of the pendant amines on the redox properties of these complexes were explored using spectroscopic and electrochemical methods. The protonation sites in such triiron clusters and their relationships were identified. The orientation of the first and second protonation processes depends on the arrangement of the second coordination sphere. The similarities and differences, due to the extended metal nuclearity, with their dinuclear counterparts [Fe2(CO)4(κ2-PPh2NR2)(μ-pdt)], were highlighted.

Growth patterns of facial muscles at the angle of the mouth: A histological study using midterm and near-term human fetuses.

At the angle of the mouth, spoke-like muscle bundles converge at the "modiolus," which is believed to appear in utero. The aim of this study was to investigate the growth of the modiolus histologically. We studied frontal histological sections of the face from 12 midterm and six near-term fetuses. At midterm, a convergence of the levator anguli oris (LAOM) and depressor anguli oris (DAOM) was frequently present, and another convergence of the LAOM with the platysma (PM) or orbicularis oris (OOM) was also often evident. At near-term, muscle fiber merging or interdigitation was classified into nine combinations, five of which were frequently seen: LAOM-PM, LAOM-DAOM, zygomaticus major (ZMM)-orbicularis oris (OOM), buccinator (BM)-LAOM, and BM-PM. These combinations existed at slightly different depths and/or sites, thus allowing the angle of the mouth to receive multiple muscles. Notably, tissues interposed between the muscle fibers were limited to a thin epimysium at each crossing or interdigitation. Therefore, the LAOM, DAOM, OOM, BM, and PM appear to form a basic configuration at birth, but the development and growth were much delayed than the classical description. The modiolus is not a specific fibromuscular structure but simply represents a cluster of muscle convergence sites. Even at meeting between an elevator and depressor, a specific fibrous structure seems unlikely to connect the epimysium for the muscle convergence. Instead, the central nervous system appears to regulate the activity of related muscles to minimize tension or friction stress at the meeting site.

Polymerization of ZBTB transcription factors regulates chromatin occupancy

BCL6, an oncogenic transcription factor (TF), forms polymers in the presence of a small-molecule molecular glue that stabilizes a complementary interface between homodimers of BCL6's broad-complex, tramtrack, and bric-à-brac (BTB) domain. The BTB domains of other proteins, including a large class of TFs, have similar architectures and symmetries, raising the possibility that additional BTB proteins self-assemble into higher-order structures. Here, we surveyed 189 human BTB proteins with a cellular fluorescent reporter assay and identified 18 ZBTB TFs that show evidence of polymerization. Through biochemical and cryoelectron microscopy (cryo-EM) studies, we demonstrate that these ZBTB TFs polymerize into filaments. We found that BTB-domain-mediated polymerization of ZBTB TFs enhances chromatin occupancy within regions containing homotypic clusters of TF binding sites, leading to repression of target genes. Our results reveal a role of higher-order structures in regulating ZBTB TFs and suggest an underappreciated role for TF polymerization in modulating gene expression.

Hillforts in the settlement system of the Sambian-Natangian culture of the South-Eastern Baltics in the 1st millennium AD

The article discusses the settlement system of the Sambian-Natangian culture of the South-Eastern Baltic region in the 1st millennium AD, the role of hillforts in it, and the structure of individual settlement centres. Hillforts are considered as dominants in the cultural landscape; together with unfortified settlements and economic zones they formed single districts. Burial grounds were located on the periphery of such centres. Individual settlement centres produced clusters of sites in the locations of amber gathering on the Kaliningrad Peninsula, along the Pregol River and the Kaliningrad Bay coast, which were important for the control of transport routes. This system was quite stable and could exist for a long period during the 1st millennium, evolving into the settlement system of the early medieval Prussians.

An Alkyne-Bridged Covalent Organic Framework Featuring Interactive Pockets for Bromine Capture.

The high degree of corrosivity and reactivity of bromine, which is released from various sources, poses a serious threat to the environment. Moreover, its coexistence with iodine forming an equilibrium compound, iodine monobromide (IBr) necessitates the selective capture of bromine from halogen mixtures. The electrophilicity of halogens to π-electron rich structures enabled us to strategically design a covalent organic framework for halogen capture, featuring a defined pore environment with localized sorption sites. The higher capture capacity of bromine (4.6 g g-1) over iodine by ~41 % shows its potential in selective capture. Spectroscopic results uncovering the preferential interaction sites are supported by theoretical investigations. The alkyne bridge is a core functionality promoting the selectivity in capture by synergistic physisorption, rationalized by the higher orbital overlap of bromine due to its smaller atomic size as well as reversible chemical interactions. The slip stacking in the structure has further promoted this phenomenon by creating clusters of molecular interaction sites with bromine intercalated between the layers. The inclusion of unsaturated moieties, i.e. triple bonds and the complementary pore geometry offer a promising design strategy for the construction of porous materials for halogen capture.

Eine Alkin‐verbrückte kovalent organische Gerüstverbindung mit interaktiven Bindungstaschen für das Einfangen von Brom

AbstractDie hohe Korrosivität und Reaktivität von Brom, welches aus verschiedenen Quellen freigesetzt wird, stellt eine ernsthafte Gefahr für die Umwelt dar. Darüber hinaus erfordert seine Koexistenz mit Iod und die daraus resultierende Gleichgewichtsverbindung Iodmonobromid (IBr) die selektive Abtrennung von Brom aus Halogengemischen. Die Elektrophilie von Halogenen gegenüber π‐elektronenreichen Strukturen ermöglichte uns die strategische Entwicklung einer kovalent organischen Gerüstverbindung für die Halogenaufnahme, die eine definierte Porenumgebung mit lokalisierten Sorptionsstellen aufweist. Die um ~41 % höhere Aufnahmekapazität von Brom (4,6 g g−1) gegenüber Iod zeigt das Potenzial für die selektive Aufnahme. Die spektroskopischen Ergebnisse, welche die bevorzugten Wechselwirkungsstellen aufzeigen, werden durch theoretische Untersuchungen gestützt. Die Alkin‐Brücke ist eine Kernfunktionalität, die die Selektivität bei der Aufnahme durch synergistische Physisorption fördert, was durch die höhere Orbitalüberlappung von Brom aufgrund seiner geringeren atomaren Größe, sowie durch reversible chemische Wechselwirkungen begründet ist. Das sogenannte „slip stacking“ in der Struktur hat dieses Phänomen weiter gefördert, indem Cluster molekularer Interaktionsstellen mit zwischen den Schichten eingelagertem Brom geschaffen wurden. Die Einführung ungesättigter Einheiten, d. h. Dreifachbindungen, und die komplementäre Porengeometrie bieten eine vielversprechende Designstrategie für die Konstruktion poröser Materialien für die Halogenaufnahme.

Prediction of Vehicle–Live Animal Crashes in Britain: Contact and Noncontact Incidents

&lt;div&gt;Animal–vehicle collisions (AVCs) can result in devastating injuries to both humans and animals. Despite significant advances in crash prediction models, there is still a significant gap when it comes to injury severity prediction models in AVCs, especially concerning small animals. It is no secret that large mammals can pose a significant threat to road safety; however, researchers tend to overlook the impact of domestic and small animals wandering along the roads. In this study, STATS19 road safety data was used containing any type of live animal, and a radial basis function (RBF) model was used to predict different severities of injury regardless of whether the animal was hit, or not. As a means of better understanding the factors contributing to severities, regression trees were used to identify and retain only the most useful predictors, removing the less useful ones. A comparison was made between the performance of the trees across a range of severity classes, and the model-fitting results were discussed. Initially, the study was unable to generate satisfactory predictions, but the optimization of the key predictors and the combination of severity classes significantly improved their accuracy. Research findings revealed factors contributing to the severities, which were discussed accordingly. Particular attention was drawn to the pressing safety issue posed by animals crossing A-class single carriageways in rural site clusters. Animals being present on those carriageways without direct vehicular contact significantly contributed to the severity of the injuries sustained. Although the majority of contributing factors were related to human behavior, no evidence of road safety education, training, or publicity interventions specifically targeting AVCs was found in the literature.&lt;/div&gt;

The Influence of Clustered DNA Damage Containing Iz/Oz and OXOdG on the Charge Transfer through the Double Helix: A Theoretical Study.

The genome-the source of life and platform of evolution-is continuously exposed to harmful factors, both extra- and intra-cellular. Their activity causes different types of DNA damage, with approximately 80 different types of lesions having been identified so far. In this paper, the influence of a clustered DNA damage site containing imidazolone (Iz) or oxazolone (Oz) and 7,8-dihydro-8-oxo-2'-deoxyguanosine (OXOdG) on the charge transfer through the double helix as well as their electronic properties were investigated. To this end, the structures of oligo-Iz, d[A1Iz2A3OXOG4A5]*d[T5C4T3C2T1], and oligo-Oz, d[A1Oz2A3OXOG4A5]*d[T5C4T3C2T1], were optimized at the M06-2X/6-D95**//M06-2X/sto-3G level of theory in the aqueous phase using the ONIOM methodology; all the discussed energies were obtained at the M06-2X/6-31++G** level of theory. The non-equilibrated and equilibrated solvent-solute interactions were taken into consideration. The following results were found: (A) In all the discussed cases, OXOdG showed a higher predisposition to radical cation formation, and B) the excess electron migration toward Iz and Oz was preferred. However, in the case of oligo-Oz, the electron transfer from Oz2 to complementary C4 was noted during vertical to adiabatic anion relaxation, while for oligo-Iz, it was settled exclusively on the Iz2 moiety. The above was reflected in the charge transfer rate constant, vertical/adiabatic ionization potential, and electron affinity energy values, as well as the charge and spin distribution. It can be postulated that imidazolone moiety formation within the CDL ds-oligo structure and its conversion to oxazolone can significantly influence the charge migration process, depending on the C2 carbon hybridization sp2 or sp3. The above can confuse the single DNA damage recognition and removal processes, cause an increase in mutagenesis, and harm the effectiveness of anticancer therapy.

Single‐Atom Long‐Range Interaction: Basic Principles and Applications

AbstractSingle‐atom catalysis involves loading the active metal onto the carrier's surface as a single‐atom. This atom is primarily bonded to the carrier surface through hetero‐atom bonding. It is important to note that the coordination environment of the metal atoms may not be the same when each dispersed active metal atom has an identical coordination environment on the carrier's surface. The utilization of single‐atom catalysts (SACs) doesn't strictly imply that a solitary metal atom with zero valency functions as the active core. Singular atoms can also engage in distant interactions with other atoms or clusters of atoms on the substrate, like electron transfer, and frequently demonstrate specific charges. The main reason for the high activity of the catalyst is the remote (i.e., long‐range) interaction of the active atom with the surrounding coordination atoms. For this reason, the study of the mechanism of long‐range interactions between multiple single‐atom sites and between single‐atom sites and atomic cluster sites has become an important and urgent task in the design and regulation of single‐atom catalyst performance.

Three families of CD4-induced antibodies are associated with the capacity of plasma from people living with HIV to mediate ADCC in presence of CD4-mimetics.

CD4-mimetics (CD4mcs) are small molecule compounds that mimic the interaction of the CD4 receptor with HIV-1 envelope glycoproteins (Env). Env from primary viruses normally samples a "closed" conformation which occludes epitopes recognized by CD4-induced (CD4i) non-neutralizing antibodies (nnAbs). CD4mcs induce conformational changes on Env resulting in the exposure of these otherwise inaccessible epitopes. Here we evaluated the capacity of plasma from a cohort of 50 people living with HIV to recognize HIV-1-infected cells and eliminate them by antibody-dependent cellular cytotoxicity (ADCC) in the presence of a potent indoline CD4mc. We observed a marked heterogeneity among plasma samples. By measuring the levels of different families of CD4i Abs, we found that the levels of anti-cluster A, anti-coreceptor binding site and anti-gp41 cluster I antibodies are responsible for plasma-mediated ADCC in presence of CD4mc.

Monodisperse Manganese-Vanadium-Oxo Clusters with Extraordinary Lithium Storage.

Although possessing well-defined nanostructures and excellent multi-electron redox properties, polyoxometalate clusters have poor intrinsic electrical conductivity and are prone to aggregation due to large surface energy, which makes them difficult to be fully utilized when applying as electrode materials for lithium-ion batteries. In this paper, monodisperse K7MnV13O38 (MnV13) clusters are achieved by rationally utilizing nano-sized high conductive carbon dots (CDs) as stabilizers. Benefiting from the fully exposed redox sites of MnV13 clusters (high utilization rate) and sufficient interfaces with carbon dots (extra interfacial energy storage), the optimized MnV13/10CDs anode delivers a high discharge capacity up to 1348 mAh g-1 at a current density of 0.1 A g-1 and exhibits superb rate/cycling capabilities. Density functional theory (DFT) calculations verify that ionic archway channels are formed between MnV13 and CDs, eliminating the bandgap and greatly improving the electron/ion conductivity of MnV13 and CDs. This paper paves a brand-new way for synthesis of monodisperse clusters and maximization of extra interfacial energy storage.

Full-Space Electric Field in Mo-Decorated Zn2In2S5 Polarization Photocatalyst for Oriented Charge Flow and Efficient Hydrogen Production.

Integration of photocatalytic hydrogen (H2) evolution with oxidative organic synthesis presents a highly attractive strategy for the simultaneous production of clean H2 fuel and high-value chemicals. However, the sluggish dynamics of photogenerated charge carriers across the photocatalysts result in low photoconversion efficiency, hindering the wide applications of such a technology. Herein, this work overcomes this limitation by inducing the full-space electric field via charge polarization engineering on a Mo cluster-decorated Zn2In2S5 (Mo-Zn2In2S5) photocatalyst. Specifically, this full-space electric field arises from a cascade of the bulk electric field (BEF) and local surface electric field (LSEF), triggering the oriented migration of photogenerated electrons from [Zn-S] regions to [In-S] regions and eventually to Mo cluster sites, ensuring efficient separation of bulk and surface charge carriers. Moreover, the surface Mo clusters induce a tip enhancement effect to optimize charge transfer behavior by augmenting electrons and proton concentration around the active sites on the basal plane of Zn2In2S5. Notably, the optimized Mo1.5-Zn2In2S5 catalyst achieves exceptional H2 and benzaldehyde production rates of 34.35 and 45.31mmol gcat -1 h-1, respectively, outperforming pristine ZnIn2S4 by 3.83- and 4.15-fold. These findings mark a significant stride in steering charge flow for enhanced photocatalytic performance.