Formation Activity Research Articles

ANTIOXIDANT, INHIBITION OF ADVANCED GLYCATION END-PRODUCT FORMATION AND ANTIMICROBIAL ACTIVITIES OF OCIMUM GRATISSIMUM (SCENT LEAF) METHANOLIC LEAF EXTRACT AGAINST Escherichia coli AND Bacillus SPP

The study investigates the antioxidant, inhibition of advanced glycation end-product formation and antimicrobial activities of methanolic leaf extract of Ocimum gratissimum. GC-MS, qualitative, antioxidant scavenging and antiglycation activities of the extract of Ocimum gratissimum were determined using standard procedures. The antimicrobial activity was evaluated by agar well diffusion method. Minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were determined using standard methods. The GC-MS analysis of Ocimum gratissimum leaf revealed the presence of 49 compounds with P –cymene been the most abundant. The phytochemical screening of the extract shows the presence of alkaloids, tannins, phenolic, flavonoids, saponins etc. The in-vitro antioxidant assay of the extract was found to have ?-carotene, lycopene, total phenolic compounds, total flavonoid compounds, reducing power and DPPH scavenging activities. The extract showed significant inhibitory effects on the formation of compounds containing two carbonyl groups and Advanced Glycated End products formation with IC50 of 75.85 ±4.87 µg/mL. Agar well diffusion assay was characterized by inhibition zones of 21.0 ± 0.30, 19.66 ± 0.20, 33.78± 0.30 and 33.25 ± 0.40 mm for Escherichia coli and Bacillus spp respectively at 250 mg/ml for Ocimum gratissimum and 25 mg/ml for tetracycline solution. The MIC values for E.coli and Bacillus spp were 33.33, 66.67, 0.78 and 0.78 for both extract and tetracycline while their MBC values were 66.67, 133.00, 1.56 and 1.56 respectively. MBC/ MIC values showed that Ocimum gratissimum extract and tetracycline had bactericidal effects. These results indicated that Ocimum gratissimum possesses antioxidant, prevents glycation and has antimicrobial activities.

Adaptive Synthesis, Supramolecular Behavior, and Biological Properties of Amphiphilic Carbosilane-Phosphonium Dendrons with Tunable Structure.

Here, we present a modular synthesis as well as physicochemical and biological evaluation of a new series of amphiphilic dendrons carrying triphenylphosphonium groups at their periphery. Within the series, the size and mutual balance of lipophilic and hydrophilic domains are systematically varied, changing the dendron shape from cylindrical to conical. In physiological solution, the dendrons exhibit very low critical micelle concentrations (2.6-4.9 μM) and form stable and uniform micelles 6-12 nm in diameter, depending on dendron shape; the results correlate well with molecular dynamics simulations. The compounds show relatively high cytotoxicity (IC50 1.2-21.0 μM) associated with micelle formation and inversely related to the size of assembled particles. Depending on their shape, the dendrons show promising results in terms of dendriplex formation and antibacterial activity. In addition to simple amphiphilic dendrons, a fluorescently labeled analogue was also prepared and utilized as an additive visualizing the dendron's cellular uptake.

Allelic Variation in gtfB–gtfC Region of Natural Variant of Streptococcus mutans Without Biofilm Formation

Streptococcus mutans is primarily found in biofilms on tooth surfaces and is associated with the development of dental caries. S. mutans synthesizes water-insoluble glucan (WIG) using sucrose as a substrate, inducing the formation of three-dimensional biofilms. WIG is produced by glucosyltransferases (GTFs) encoded by the tandem and highly homologous gtfB and gtfC genes. Conversely, the homologous recombination of gtfB and gtfC readily happens, producing natural variants without WIG. These WIG− variants are thought to have ecologically pleiotropic functions; however, the molecular basis for their appearance is unclear. This study aimed to determine the sequence of the gtfB–gtfC regions of WIG− variants. We sequenced the gtfB–gtfC regions of 23 WIG− variants derived from S. mutans UA159 and revealed the presence of five alleles and four types of single homologous recombination patterns. Regardless of the allele type, the WIG− variants showed low biofilm formation and GTF activity. To the best of our knowledge, this is the first study to report the presence of alleles in WIG− variants. These findings provide important information for explaining the appearance of mechanisms in WIG− variants.

Crimson Behemoth: A massive clumpy structure hosting a dusty AGN at z=4.91

Abstract The current paradigm for the co-evolution of galaxies and their supermassive black holes postulates that dust-obscured active galactic nuclei (AGNs) represent a transitional phase towards a more luminous and unobscured state. However, our understanding of dusty AGNs and their host galaxies at early cosmic times is inadequate due to observational limitations. Here, we present JWST observations of CID-931, an X-ray-detected AGN at a spectroscopic redshift of $z_{\rm spec}=4.91$. Multiband NIRCam imaging from the COSMOS-Web program reveals an unresolved red core, similar to JWST-discovered dusty AGNs. Strikingly, the red core is surrounded by at least eight massive star-forming clumps spread over ${1{^{\prime \prime}_{.}}6} \approx 10\,\,{\rm kpc}$, each of which has a stellar mass of $10^9$–$10^{10}\, M_{\odot }$ and a radius of $\sim$0.1–1 kpc. The whole system amounts to $10^{11}\, M_{\odot }$ in stellar mass, higher than typical star-forming galaxies at the same epoch. In this system, gas inflows and/or complex merger events may trigger clump formation and AGN activity, thus leading to the rapid formation of a massive galaxy hosting a supermassive black hole. Future follow-up observations will provide new insights into the evolution of the galaxy–black hole relationship during such transitional phases in the early universe.

A molecular module connects abscisic acid with auxin signals to facilitate seasonal wood formation in Populus.

Perennial trees have a recurring annual cycle of wood formation in response to environmental fluctuations. However, the precise molecular mechanisms that regulate the seasonal formation of wood remain poorly understood. Our prior study indicates that VCM1 and VCM2 play a vital role in regulating the activity of the vascular cambium by controlling the auxin homoeostasis of the cambium zone in Populus. This study indicates that abscisic acid (ABA) affects the expression of VCM1 and VCM2, which display seasonal fluctuations in relation to photoperiod changes. ABA-responsive transcription factors AREB4 and AREB13, which are predominantly expressed in stem secondary vascular tissue, bind to VCM1 and VCM2 promoters to induce their expression. Seasonal changes in the photoperiod affect the ABA amount, which is linked to auxin-regulated cambium activity via the functions of VCM1 and VCM2. Thus, the study reveals that AREB4/AREB13-VCM1/VCM2-PIN5b acts as a molecular module connecting ABA and auxin signals to control vascular cambium activity in seasonal wood formation.

Cyclic di-GMP incorporates the transcriptional factor FleQ03 in Pseudomonas syringae MB03 to elicit biofilm-dependent resistance in response to Caenorhabditis elegans predation

Bacteria usually form biofilms as a defense mechanism against predation by bacterivorous nematodes. In this context, the second messenger c-di-GMP from the wild-type Pseudomonas syringae MB03 actuates the transcriptional factor FleQ03 to elicit biofilm-dependent nematicidal activity against Caenorhabditis elegans N2. P. syringae MB03 cells exhibited nematicidal activity and c-di-GMP content in P. syringae MB03 cells was increased after feeding to nematodes. Expression of a diguanylate cyclase (DGC) gene in P. syringae MB03 resulted in an increased c-di-GMP content, biofilm yield and nematicidal activity, whereas converse effects were obtained when expressing a phosphodiesterase (PDE) gene. Molecular docking and isothermal titration calorimetry assays verified the affinity activity between c-di-GMP and the FleQ03 protein. The disruption of the fleQ03 gene in P. syringae MB03, while increasing c-di-GMP content, significantly diminished both biofilm formation and nematicidal activity. Interestingly, P. syringae MB03 formed a full-body biofilm around the worms against predation, probably extending from the tail to the head, whereas it was not observed in the fleQ03 gene disrupted cells. Thus, we hypothesized that c-di-GMP incorporated FleQ03 to reinforce bacterial biofilm and biofilm-dependent pathogenicity in response to C. elegans predation, providing insights into a possible means of resisting bacterivorous nematodes by bacteria in natural ecosystems.

The ALMA-CRISTAL Survey: Spatially Resolved Star Formation Activity and Dust Content in 4 < z < 6 Star-forming Galaxies

Using a combination of Hubble Space Telescope (HST), JWST, and Atacama Large Millimeter/submillimeter Array (ALMA) data, we perform spatially resolved spectral energy distributions (SED) fitting of fourteen 4 < z < 6 ultraviolet (UV)-selected main-sequence galaxies targeted by the ALMA Large Program [C ii] Resolved ISM in Star-forming Galaxies. We consistently model the emission from stars and dust in ∼0.5–1 kpc spatial bins to obtain maps of their physical properties. We find no offsets between the stellar masses (M *) and star formation rates (SFRs) derived from their global emission and those from adding up the values in our spatial bins, suggesting there is no bias of outshining by young stars on the derived global properties. We show that ALMA observations are important to derive robust parameter maps because they reduce the uncertainties in L dust (hence, AV and SFR). Using these maps, we explore the resolved star-forming main sequence for z ∼ 5 galaxies, finding that this relation persists in typical star-forming galaxies in the early Universe. We find less obscured star formation where the M * (and SFR) surface densities are highest, typically in the central regions, contrary to the global relation between these parameters. We speculate this could be caused by feedback driving gas and dust out of these regions. However, more observations of IR luminosities with ALMA are needed to verify this. Finally, we test empirical SFR prescriptions based on the UV+IR and [C ii] line luminosity, finding they work well at the scales probed (approximately kiloparsec). Our work demonstrates the usefulness of joint HST-, JWST-, and ALMA-resolved SED modeling analyses at high redshift.

RIGEL: Simulating dwarf galaxies at solar mass resolution with radiative transfer and feedback from individual massive stars

Context. Feedback from stars in the form of radiation, stellar winds, and supernovae is crucial to regulating the star formation activity of galaxies. Dwarf galaxies are especially susceptible to these processes, making them an ideal test bed for studying the effects of stellar feedback in detail. Recent numerical models have aimed to resolve the interstellar medium (ISM) in dwarf galaxies with a very high resolution of several solar masses. However, when it comes to modeling the radiative feedback from stars, many models opt for simplified approaches instead of explicitly solving radiative transfer (RT) because of the computational complexity involved. Aims. We introduce the Realistic ISM modeling in Galaxy Evolution and Lifecycles (RIGEL) model, a novel framework to self-consistently model the effects of stellar feedback in the multiphase ISM of dwarf galaxies with explicit RT on a star-by-star basis. Methods. The RIGEL model integrates detailed implementations of feedback from individual massive stars into the state-of-the-art radiation-hydrodynamics code, AREPO-RT. It forms individual massive stars from the resolved multiphase ISM by sampling the initial mass function and tracks their evolution individually. The lifetimes, photon production rates, mass-loss rates, and wind velocities of these stars are determined by their initial masses and metallicities based on a library that incorporates a variety of stellar models. The RT equations are solved explicitly in seven spectral bins accounting for the infrared to He II ionizing bands, using a moment-base scheme with the M1 closure relation. The thermochemistry model tracks the nonequilibrium H, He chemistry as well as the equilibrium abundance of C I, C II, O I, O II, and CO in the irradiated ISM to capture the thermodynamics of all ISM phases, from cold molecular gas to hot ionized gas. Results. We evaluated the performance of the RIGEL model using 1 M⊙ resolution simulations of isolated dwarf galaxies. We found that the star formation rate (SFR) and interstellar radiation field (ISRF) show strong positive correlations with the metallicity of the galaxy. Photoionization and photoheating can reduce the SFR by an order of magnitude by removing the available cold, dense gas fuel for star formation. The presence of ISRF also significantly changes the thermal structure of the ISM. Radiative feedback occurs immediately after the birth of massive stars and rapidly disperses the molecular clouds within 1 Myr. As a consequence, radiative feedback reduces the age spread of star clusters to less than 2 Myr, prohibits the formation of massive star clusters, and shapes the cluster initial mass function to a steep power-law form with a slope of ∼ − 2. The mass-loading factor (measured at z = 1 kpc) of the fiducial galaxy has a median of ηM ∼ 50, while turning off radiative feedback reduces this factor by an order of magnitude. Conclusions. We demonstrate that RIGEL effectively captures the nonlinear coupling of early radiative feedback and supernova feedback in the multiphase ISM of dwarf galaxies. This novel framework enables the utilization of a comprehensive stellar feedback and ISM model in cosmological simulations of dwarf galaxies and various galactic environments spanning a wide dynamic range in both space and time.

Radio–FIR correlation: A probe into cosmic ray propagation in the nearby galaxy IC 342

Resolved studies of the correlation between the radio and far-infrared (FIR) emission from galaxies at different frequencies can unveil the interplay between star formation and the relativistic interstellar medium (ISM). Thanks to the LOFAR LoTSS observations combined with VLA, Herschel, and WISE data, we study the role of cosmic rays and magnetic fields in the radio–FIR correlation on scales of ≳200 pc in the nearby galaxy IC 342. The thermal emission traced by the 22 μm emission, constitutes about 6%, 13%, and 30% of the observed radio emission at 0.14, 1.4, and 4.8 GHz, respectively, in star-forming regions and less in other parts. The nonthermal spectral index becomes flatter at frequencies lower than 1.4 GHz (αn = −0.51 ± 0.09, Sν ∝ ναn) than between 1.4 and 4.8 GHz (αn = −1.06 ± 0.19) on average, and this flattening occurs not only in star-forming regions but also in the diffuse ISM. The radio–FIR correlation holds at all radio frequencies; however, it is tighter at higher radio frequencies. A multi-scale analysis shows that this correlation cannot be maintained on small scales due to diffusion of cosmic ray electrons (CREs). The correlation breaks at a larger scale (≃320 pc) at 0.14 GHz than at 1.4 GHz (≃200 pc), indicating that the CREs traced at lower frequencies have diffused a longer path in the ISM. We find that the energy index of CREs becomes flatter in star-forming regions, in agreement with previous studies. Cooling of CREs due to the magnetic field is evident globally only after compensating for the effect of star formation activity that both accelerates CREs and amplifies magnetic fields. Compared with other nearby galaxies, we show that the smallest scale of the radio–FIR correlation is proportional to the propagation length of the CREs on which the ordered magnetic field has an important effect.

Understanding university English instructors’ assessment literacy: a formative assessment perspective

Formative assessment is a powerful approach to inform, direct, and enhance teaching and learning. To deploy it in classrooms, teachers are expected to be assessment-capable. However, few studies have explored the extent to which teachers are literate in formative assessment applications and their levels of literacy, especially in Chinese tertiary settings. This study examined Chinese university English instructors’ assessment literacy by investigating what three participants knew, thought about, and how they applied formative assessment. A knowledge-conception-practice framework was applied to explore assessment literacy in the four formative assessment processes (i.e., design, use, interpretation, and communication) to engage student learning. Individual interviews, classroom observations, and supplementary documents were adopted as instruments for data collection. Through iterative and comparative thematic analysis, findings revealed that notwithstanding variations, all three instructors possessed basic formative assessment knowledge and were willing to design and conduct formative assessment-related activities for students’ learning engagement and enhancement. However, they held product-oriented rather than process-oriented mindsets when designing, using, interpreting, and communicating formative assessment. They also lacked sufficient assessment knowledge and strategies to effectively engage students in self-regulated learning through learner-centered task design, success criteria, and process-oriented feedback. Lastly, the study discussed theoretical and pedagogical implications regarding how to conceptualize and develop English instructors’ formative assessment literacy in mainland China and beyond.

Applications of nickel-containing structured microfibrous catalysts for the process of propane hydrogenolysis

This work evaluates the possibility of using nickel-containing structured glass fiber catalysts (Ni/GFC) for the process of hydrogenolysis of gas condensate (GC) into transportable components of natural gas, which will increase the efficiency of GC processing and contribute to the development of more cost-effective technologies in the oil-gas industry. Ni/GFC samples with Ni content of 5, 10 and 15% wt. were synthesized by surface thermal synthesis (STS). An industrial granular catalyst with a mass Ni content of 16% was used to compare the catalytic activity of the obtained catalysts. The highest activity and selectivity of methane formation is observed on the 10% Ni/ GFC catalyst, by these parameters it is superior not only to other GFCs, but also the traditional granular catalyst.

Simba-EoR: early galaxy formation in the simba simulation including a new sub-grid interstellar medium model

ABSTRACT We update the dust model present within the simba galaxy simulations with a self-consistent framework for the co-evolution of dust and molecular hydrogen populations in the interstellar medium, and use this to explore $z \ge 6$ galaxy evolution. In addition to tracking the evolution of dust and molecular hydrogen abundances, our model fully integrates these species into the simba simulation, explicitly modelling their impact on physical processes such as star formation and cooling through the inclusion of a novel two-phase sub-grid model for interstellar gas. Running two cosmological simulations down to $z \sim 6$ we find that our simba-EoR model displays a generally tighter concordance with observational data than fiducial simba. Additionally we observe that our simba-EoR models increase star formation activity at early epochs, producing larger dust-to-gas ratios consequently. Finally, we discover a significant population of hot dust at $\sim 100$ K, aligning with contemporaneous observations of high-redshift dusty galaxies, alongside the large $\sim 20$ K population typically identified.

An Update on Molecular Mechanisms of Scarring-A Narrative Review.

Fibroblasts, the principal cellular mediators of connective tissue remodeling, play a crucial role in the formation of physiological and pathological scars. Understanding the intricate interplay between fibroblasts and other cellular and molecular components is essential for elucidating the underlying mechanisms driving scar formation. Hypertrophic scars, keloids and atrophic scars arise from dysregulated wound healing processes characterized by persistent inflammation, aberrant collagen deposition, and impaired extracellular matrix remodeling. Fibroblasts play a central role in the pathogenesis of such pathological scars, driving aberrant extracellular matrix remodeling, subsequently contributing to the formation of raised or depressed fibrotic lesions. The investigation of complex interactions between fibroblasts and the microenvironment is crucial for developing targeted therapeutic interventions aimed at modulating fibroblast activity and improving clinical outcomes in patients with pathological scars. Further research into the molecular pathways governing fibroblast behavior and their heterogeneity holds promise for advancing scar management strategies. This narrative review was performed to shed light on the mechanisms behind scar formation, with a special focus on the role of fibroblasts in the formation of different types of scars, providing insights into the pathophysiology of these conditions. Through the analysis of current knowledge, this review seeks to identify the key cellular and molecular mechanisms involved in fibroblast activation, collagen synthesis, and extracellular matrix remodeling in hypertrophic scar, keloid, or atrophic scar formation.

Boosting Dry Reforming of Methane Over NiCo/CeO2 Catalysts Treated by Hydrogen Plasma

ABSTRACTNickel (Ni)‐based catalysts are prospective materials for dry reforming of methane (DRM) reaction, but suffer from coke formation and limited activity for CO2 conversion. To improve the reactivity of Ni‐based catalysts, a promising strategy is introducing cobalt (Co) metal. Here, we construct highly efficient NiCo sites on CeO2 support by H2 plasma, which enables the catalyst to obtain a remarkable increase in DRM reaction than the samples treated by conventional H2 reduction. H2 plasma treatment results in the formation of highly dispersed NiCo alloy nanoparticles and high‐concentration oxygen vacancy. These features create large numbers of highly active sites to boost the activation of CH4 and especially CO2 and their catalytic reactions, resulting in strong coke resistance in the DRM reaction.

A Closer Look at Dwarf Galaxies Exhibiting Mid-infrared Variability: Active Galactic Nuclei Confirmation and Comparison With Nonvariable Dwarf Galaxies

Detecting active black holes in dwarf galaxies has proven to be a challenge due to their small size and weak electromagnetic signatures. Mid-infrared variability has emerged as a promising tool that can be used to detect active low-mass black holes in dwarf galaxies. We analyzed 10.4 yr of photometry from the AllWISE/NEOWISE multiepoch catalogs, identifying 25 objects with active galactic nuclei (AGN)-like variability. Independent confirmation of AGN activity was found in 68% of these objects using optical and near-infrared diagnostics. Notably, we discover a near-infrared coronal line [S ix] λ 1.252 μm in J1205, the galaxy with the lowest stellar mass (log M * = 7.5 M ⊙) and low metallicity (12 + log(O/H) = 7.46) in our sample. Additionally, we find broad Paα potentially from the broad-line region in two targets, and their implied black hole masses are consistent with black hole-stellar mass relations. Comparing nonvariable galaxies with similar stellar masses and Wide-field Infrared Survey Explorer W1 − W2 colors, we find no clear trends between variability and large-scale galaxy properties. However, we find that AGN activity likely causes redder W1 − W2 colors in variable targets, while for the nonvariable galaxies, the contribution stems from strong star formation activity. A high incidence of optical broad lines was also observed in variable targets. Our results suggest that mid-infrared variability is an effective method for detecting AGN activity in low-mass galaxies and can help uncover a larger sample of active low-mass (<106 M ⊙) black holes in the Universe.

Selective CO2 Reduction Electrocatalysis Using AgCu Nanoalloys Prepared by a "Host-Guest" Method.

Multimetallic nanoalloy catalysts have attracted considerable interest for enhancing the efficiency and selectivity of many electrochemically driven chemical processes. However, the preparation of homogeneous bimetallic alloy nanoparticles remains a challenge. Here, we present a room-temperature and scalable, host-guest approach for synthesis of dilute Cu in Ag alloy nanoparticles. In this approach, an ionic silver bromide precursor harboring exogenous Cu cations is reduced to yield ∼20 nm diameter AgCu alloy nanoparticles wherein the % Cu loading can be tuned precisely. AgCu nanoparticles with a 5% nominal loading of Cu exhibit peak activity (-0.23 mA/cm2 normalized partial current density) and selectivity (83.2% faradaic efficiency) for CO product formation from electrocatalytic reduction of CO2 at mild overpotentials. These AgCu nanoalloys exhibit a higher mass activity compared to Ag- and Cu-containing nanomaterials used for similar electrocatalytic transformations. Our host-guest synthesis platform holds promise for production of other nanoalloys with relevance in electrocatalysis and optics.

The star formation history of the first bulge fossil fragment candidate Terzan 5

Terzan 5 and Liller 1 are the only bulge stellar clusters hosting multi-iron and multi-age stellar populations. They are therefore claimed to constitute a novel class of astrophysical objects: the fossils of massive star-forming clumps that possibly sank to the center of the Milky Way and contributed to the formation of the bulge. This is based on the hypothesis that the ancient clumps were able to retain iron-enriched supernova ejecta, later giving rise to younger and more metal-rich populations. A way to investigate this scenario is reconstructing their star formation histories (SFHs) and proving a prolonged and multiepisode star formation activity. Leveraging ground- and space-based high-resolution images, we derived the SFH of Terzan 5 by employing the color-magnitude diagram fitting routine SFERA. The best-fit solution predicts an old, main peak occurred between 12 and $13\,$Gyr ago that generated $70\,&lt;!PCT!&gt;$ of the current stellar mass, followed by a lower-rate star formation activity with two main additional bursts. These results indicate that Terzan 5, similarly to Liller 1, experienced a prolonged, multiepisode star formation activity, fueled by metal-enriched gas deposited in its central regions, in agreement with the expectations of a self-enrichment scenario in a primordial massive clump.

Structures of a DNA Polymerase Caught while Incorporating Responsive Dual-Functional Nucleotide Probes.

Functionalizing nucleic acids using DNA polymerases is essential in biophysical and biotechnology applications. This study focuses on understanding how DNA polymerases recognize and incorporate nucleotides with diverse chemical modifications, aiming to develop advanced nucleotide probes. We present the crystal structures of ternary complexes of Thermus aquaticus DNA polymerase (KlenTaq) with C5-heterocycle-modified environment-sensitive 2'-deoxyuridine-5'-triphosphate (dUTP) probes. These nucleotides include SedUTP, BFdUTP and FBFdUTP, which bear selenophene, benzofuran and fluorobenzofuran, respectively, at the C5 position of uracil, and exhibit high conformational sensitivity. SedUTP and FBFdUTP serve as dual-app probes, combining a fluorophore with X-ray anomalous scattering Se or 19F NMR labels. Our study reveals that the size of the heterocycle influences how DNA polymerase families A and B incorporate these modified nucleotides during single nucleotide incorporation and primer extension reactions. Remarkably, FBFdUTP's responsiveness enabled real-time monitoring of the binary complex formation and polymerase activity through fluorescence and 19F NMR. Comparative analysis of incorporation profiles, fluorescence, 19F NMR data, and crystal structures of ternary complexes highlights the enzyme's plasticity. Key insights are provided into the role of gatekeeper amino acids (Arg660 and Arg587) in accommodating and processing these modified substrates, offering a structural basis for next-generation nucleotide probe development.

Structures of a DNA Polymerase Caught while Incorporating Responsive Dual‐Functional Nucleotide Probes

Functionalizing nucleic acids using DNA polymerases is essential in biophysical and biotechnology applications. This study focuses on understanding how DNA polymerases recognize and incorporate nucleotides with diverse chemical modifications, aiming to develop advanced nucleotide probes. We present the crystal structures of ternary complexes of Thermus aquaticus DNA polymerase (KlenTaq) with C5‐heterocycle‐modified environment‐sensitive 2′‐deoxyuridine‐5′‐triphosphate (dUTP) probes. These nucleotides include SedUTP, BFdUTP and FBFdUTP, which bear selenophene, benzofuran and fluorobenzofuran, respectively, at the C5 position of uracil, and exhibit high conformational sensitivity. SedUTP and FBFdUTP serve as dual‐app probes, combining a fluorophore with X‐ray anomalous scattering Se or 19F NMR labels. Our study reveals that the size of the heterocycle influences how DNA polymerase families A and B incorporate these modified nucleotides during single nucleotide incorporation and primer extension reactions. Remarkably, FBFdUTP's responsiveness enabled real‐time monitoring of the binary complex formation and polymerase activity through fluorescence and 19F NMR. Comparative analysis of incorporation profiles, fluorescence, 19F NMR data, and crystal structures of ternary complexes highlights the enzyme's plasticity. Key insights are provided into the role of gatekeeper amino acids (Arg660 and Arg587) in accommodating and processing these modified substrates, offering a structural basis for next‐generation nucleotide probe development.

Implementation strategies to improve adoption of unmet social needs screening and referrals in care management using enabling technologies: study protocol for a cluster randomized trial.

Background Adverse social determinants of health contribute to health inequities. Practice guidelines now recommend incorporating patient unmet social needs into patient care, and payors increasingly reimburse for screening and providing related referrals to community organizations. Emergent electronic health record (EHR)-based tools can enable clinical-community linkages, but their adoption commonly faces workflow and infrastructure barriers. Targeted implementation support such as training, championship, practice facilitation, and audit and feedback, can enhance such tools' adoption, but no prior research has assessed such strategies' impact on the adoption of 'enabling technologies' supporting clinical-community linkages. This study will test whether providing targeted implementation support to safety-net primary care health center care management teams improves the sustained adoption of EHR-based enabling technologies used to 1) screen for social needs and 2) link patients to community organizations. Methods Formative evaluation of barriers and facilitators to adopting EHR-enabled social needs referrals and ascertainment of services received will include semi-structured interviews and a 'guided tour' of enabling technology used by care managers serving patients with complex health and/or social needs. A modified Delphi process conducted with care management staff and subject matter experts will then inform the development of an intervention targeting adoption of social risk EHR-enabled tools. The intervention will be piloted in three health centers, refined, then tested in a pragmatic stepped-wedge cluster-randomized trial in 20 health centers (five wedges of four health centers) that provide care management to high-risk patients with social needs. Discussion This study is among the first to evaluate an intervention designed to support care management teams' adoption of enabling technologies to increase clinical-community linkages. It was funded in September 2023 by the National Institute of Nursing Research. Formative activities will take place from January to June 2024, the intervention will be developed in July-December 2024, the pilot study will be conducted from January-March 2025, and the cluster-randomized trial will occur from July 2025 -September 2026. Study data will be analyzed and results disseminated in 2027-2028. Study results have the potential to improve clinical-community linkages and in so doing to advance health equity. Trial registration Clinicaltrials.gov registration # NCT06489002. Registered July 5, 2024, https//clinicaltrials.gov/study/NCT06489002?term=NCT06489002&rank=1.